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transcriptome analysis

11032 relationships annotated with this phrase. Showing first 500 of 11032.
Source entity Relationship Target entity Species
729 DEGs in OXmiR400 plants include 315 upregulated and 414 downregulated genes Arabidopsis thaliana
437 DEGs between OXmiR400 and OXrPPR1 include 197 upregulated and 240 downregulated genes Arabidopsis thaliana
differentially expressed genes between stone cells and cortical parenchyma revealed 424 transcripts upregulated in cortical parenchyma cells Picea sitchensis
small number of DEGs (241 genes; approximately 1.8% of the whole gene sets) were detected between the two host species Colletotrichum orbiculare
PC2 explained 13.4% of the original variance Picea sitchensis
comparative transcriptome analyses were performed between stone cells and cortical parenchyma cells Picea sitchensis
differentially expressed genes (DEGs) identified using edgeR (glmTreat test) Colletotrichum orbiculare
comparative transcriptome analyses were performed between R and S trees Picea sitchensis
(APC1, PC1, AT5G17480) and PC2 accounted for 63.1% of the original variance Picea sitchensis
Affymetrix GeneChips allowed comparison of Rorippa species data with Arabidopsis data Rorippa amphibia; Rorippa sylvestris; Arabidopsis thaliana
second principal component (PC2) separated stone cells from cortical parenchyma cells Picea sitchensis
PC2 explained 14.7% of the original variance Picea sitchensis
differentially expressed genes between stone cells and cortical parenchyma revealed 486 transcripts upregulated in cortical parenchyma cells Picea sitchensis
large cluster of upregulated genes was found in stone cells from R genotype Picea sitchensis
OXmiR400 transgenic plants have 729 differentially expressed genes (DEGs) relative to WT plants Arabidopsis thaliana
differentially expressed transcripts in stone cells from R genotype were distinct from other transcriptomes Picea sitchensis
(APC1, PC1, AT5G17480) explained 55.1% of the original variance Picea sitchensis
RNA-seq performed on root cap, meristem, and elongation zone of WT barley roots Hordeum vulgare
transcriptome libraries included two genotypes, two tissue types, and three biological replicates Picea sitchensis
differentially expressed genes between stone cells and cortical parenchyma revealed 1129 transcripts significantly upregulated in stone cells Picea sitchensis
significantly differentially expressed genes are identified by RNA-Seq differential expression analysis Gossypium hirsutum
Principal component analysis (PCA) of variation revealed reproducible separation of transcriptome clusters between genotype and time points Picea sitchensis
COT samples exhibit higher variance throughout time course Lepidium sativum
PC2 separated TP1, TP2, TP3 from TP4 Picea sitchensis
principal component analysis (PCA) revealed reproducible separation between genotype and cell-type Picea sitchensis
RIP RNA samples were submitted to RNAseq Arabidopsis thaliana
transcriptome differences separated R and S genotypes Picea sitchensis
differentially expressed transcripts showed clear separation between genotypes and cell-type transcriptomes Picea sitchensis
Functional categorization analysis (using Pageman) was performed for transcripts changing in abundance in response to stress for both (AOX1A, ATAOX1A, AtHSR3, HSR3, AT3G22370) and rpoTmp plants Arabidopsis thaliana
replicates were grouped together in four distinct clusters Picea sitchensis
Pearson's correlation coefficient was approximately 0.99
retooled INTACT can enable high-resolution monitoring of nuclear transcriptome Oryza sativa L.
coverage for these RNAs was more evenly distributed along transcription unit Oryza sativa
DEGs upregulated in OXrPPR1 are also differentially expressed but in opposite direction in OXmiR400 plants Arabidopsis thaliana
one biological replicate for R genotype in TP1 did not cluster with other samples Picea sitchensis
454 pyrosequencing compares expression profiles in each cell type Hieracium praealtum
average distribution of RNA-seq reads across all individual transcripts detected in nuclear and poly(A) + RNA with >5 rpkM illuminated bias in RNA-seq reads near the 5′ end of nuclear transcripts in contrast to the more equally distributed reads across the entire transcription unit in poly(A) + RNA Oryza sativa
transcriptional signatures of enlarged aposporous initial (AI) cells were identified by comparing with apomictic ovaries at specific developmental stages Hieracium praealtum
microarray studies and statistical analyses described in detail in Supplementary Data Arabidopsis thaliana
cluster analysis of transcript abundance patterns showed five clearly distinct clusters Lepidium sativum
DAVID GO cluster tool is widely used transcriptome data interpretation tool Arabidopsis thaliana
gl3–sst (SIM, AT5G04470) trichomes were used to generate probes for hybridization to Affymetrix (ATH1, AT4G32980) GeneChips Arabidopsis thaliana
subsampling of the libraries confirmed that each library had reached a saturation of transcripts identified as present in each population Oryza sativa
differential gene expression analysis in aposporous initial (AI) and somatic ovule (SO) cells and early aposporous embryo (EAE) sacs was conducted using Illumina sequencing platform Hieracium praealtum
soybean lincRNAs were available for analysis with 6,018 loci Glycine max
poly(A) + RNA had about 16,500 protein-coding transcripts detected Oryza sativa
young stems of LA3560 (Wo) and non-woolly segregants (WT) were utilized to construct cDNA libraries
INTACT was used to evaluate complete nuclear transcriptome by RNA-seq Oryza sativa
remaining reads were mapped to exons with ≤2 mismatches to the Nipponbare genome (IRGSP-1.0.30) Oryza sativa
strand-specific RNA-Seq data were not available for sperm cells and young (AtEMF2, CYR1, EMF2, VEF2, AT5G51230) mutant panicles Oryza sativa
high-throughput technologies offer opportunity for coding and noncoding transcript detection and quantification
nuclear RNA samples had greater proportions of introns and 5′ UTRs (flanking regions) Oryza sativa
17 genes showed expression differences greater than 100-fold Zea mays
Red and blue boxes indicate up-regulated and down-regulated transcripts, respectively, according to the color scale for (AIRP3, AtAIRP3, LOG2, AT3G09770) fold changes Arabidopsis thaliana
most fold changes showed that there was less than 10% difference in the fold change magnitude between the two mutant backgrounds Arabidopsis thaliana
dominance of unique changes in the double mutant means that the transcriptome changes at a functional level were defined by these unique responses Arabidopsis thaliana
RNA-seq analysis identified 622 other genes differentially expressed in sulki1-8 versus Ler/ (ATKAS2, FAB1, KAS2, AT1G74960) NIL that did not show significant expression differences in versus Ler/ NIL Arabidopsis thaliana
unique response in (AOX1A, ATAOX1A, AtHSR3, HSR3, AT3G22370) rpoTmp double mutants was not a sum of the changes observed in each single mutant Arabidopsis thaliana
nuclear RNA libraries had somewhat greater variation than poly(A) + RNA libraries Oryza sativa
laser-capture microdissection in conjunction with 454 pyrosequencing was used to examine transcripts in enlarging AI cells, early aposporous embryo (EAE) sacs, and somatic ovule (SO) cells Hieracium praealtum
transcriptional signatures of enlarged aposporous initial (AI) cells were identified by comparing with deletion mutants that have lost the capacity to form AI cells Hieracium praealtum
Haberlea rhodopensis transcriptome reads were pseudoaligned to the assembly using kallisto program Haberlea rhodopensis
differentially expressed (DE) genes were grouped into simple expression clusters based on point of maximal expression Xerophyta humilis
PCA analysis grouped Q2;1, Q3;1, and Q3;2 close together and separate from wild-type, Q1;1, and Q2;2
Three-way principle component analysis (PCA) was carried out for all microarray gene chips, showing a clear separation on PCA1 (64.9%) for (AOX1A, ATAOX1A, AtHSR3, HSR3, AT3G22370) and rpoTmp under MLD conditions Arabidopsis thaliana
principal component analysis (PCA) identifies eigenvectors with greatest influence on sample variance Lepidium sativum
mRNAs with introns had few nuclear RNA reads map to intervening regions Oryza sativa
Three nucleus-enriched transcripts illustrate read mapping pattern in genome browser views: DELLA protein SLENDER LEAF (RICE1, AT3G11770) (SLR1), ARG DECARBOXYLASE, and ABC TRANSPORTER B FAMILY MEMBER9 Oryza sativa
overlap in genes changing in the (AOX1A, ATAOX1A, AtHSR3, HSR3, AT3G22370) rpoTmp mutants compared with and rpoTmp was very small Arabidopsis thaliana
mRNAs were highly enriched in nucleus as compared to the poly(A) + RNA pool Oryza sativa
read coverage averaged for all poly(A) + RNAs uncovered modest 5′-end bias and a more pronounced 3′-end bias Oryza sativa
strand-specific RNA-seq data from seedling and drought-stressed samples enabled extraction of strand information for 464 lincRNA loci Oryza sativa
most available transcriptome data interpretation tools are based on enrichment or clustering analysis Arabidopsis thaliana
RNA-seq was performed on X. humilis leaves harvested at five relative water contents (RWCs) during vegetative desiccation Xerophyta humilis
RNA sequencing of 240 lettuce accessions generated expression data for 22,039 genes Lactuca sativa
correlation matrix heatmap indicated that transcriptome responses changed substantially between 8 and 16 hpi in all three accessions Brachipodium distachyon
3′ mRNA-seq-based transcriptome analysis identified 1164 differentially expressed genes (DEGs) between BdWRKY38-ox and wild-type Bd21 Brachipodium distachyon
principal component 2 (PC2) separates field cold acclimation (F-CA) from artificial cold acclimation (A-CA) and artificial cold acclimation with UVB (A-CA + UVB)
obtained RNA-seq reads were mapped to Bd21 reference genome Brachipodium distachyon
genes showing no or very low expression are removed using HTSfilter R package Petunia axillaris; Petunia exserta; Petunia parodii
DYGs in Bd3-1 overlapped with DYGs in Bd21 Brachipodium distachyon
RK16331–13 line subjected to three independent hybridizations Oryza sativa
two-module discovery pipeline allows one to make good use of all available plant-microbe interaction transcriptome data
20 WRKY genes were identified as GRN hubs Brachipodium distachyon
Controls and Phe-treated flowers shared high correlation and formed one cluster depicting small transcriptional changes Chrysanthemum morifolium
sequencing yielded ~54 to ~95 million read pairs per library Lotus japonicus
WGCNA method was used to classify expression patterns of transcription factors Zea mays
predictor performance was slightly better in leaf and root samples Arabidopsis thaliana
bud stage (0 DAP) had 240 DEGs Aethionema arabicum
3' mRNA sequencing was performed on mesophyll, bundle sheath and veinal cells Oryza sativa
ten WRKY genes were hubs in GRNs of the resistant accessions Brachipodium distachyon
BdWRKY36 and BdWRKY38 were shared between Bd3-1 and Tek-3 Brachipodium distachyon
differentially expressed genes (DEGs) identified in Experiment II (A-NA versus A-CA)
gene regulatory network (GRN) analysis was performed in Bd3-1, Tek-3 and Bd21 Brachipodium distachyon
BdWRKY25 was specific to Bd3-1 Brachipodium distachyon
gene expression samples cluster more similarly than by species Petunia axillaris; Petunia exserta; Petunia parodii
sRNA sequencing combined with mRNA/lncRNA sequencing Arabidopsis thaliana
RNA-seq libraries separated primarily by experiment (tissue of origin) Xerophyta humilis
GRNs in Bd21, Bd3-1 and Tek-3 were composed of 496, 692 and 532 nodes with 10, 8 and 16 hub WRKY genes, respectively Brachipodium distachyon
leaf tissue samples at higher water contents (100%, 80% and 60% RWC) showed clear separation from samples during later stages of desiccation (40% and 5% RWC) Xerophyta humilis
118 genes were expressed at steady-state in both BdWRKY38-ox and wild-type Bd21 Brachipodium distachyon
The expression of (PRLIP2, AT5G24200) was still 26-fold higher in complementation line #2 than in the wild type Arabidopsis thaliana
3' mRNA sequencing obtained from each cell type 24–36 million reads from four or five biological replicates Oryza sativa
Biological replicates of control infected flowers showed high correlation and grouped far apart in principal component analysis (PCA) Chrysanthemum morifolium
DEGs were clustered into seven semi-distinct groups Marchantia inflexa
predictor performed just moderately well on single-cell RNA-Seq samples Arabidopsis thaliana
rice seedling transcriptome is analyzed by STAIR pipeline Oryza sativa L. ssp. japonica
mutant anther samples at stages 8a–9 are obviously separated from corresponding WT anther samples in principal-component analysis Zea mays
KEGG pathways enriched in Experiment I (F-NA versus F-CA)
RNA sequencing (RNA-seq) analysis was performed using bHLH6 OV, (ATSPX4, SPX4, AT5G15330) and WT plants Oryza sativa
AtGenExpress project measured transcriptomes of all major Arabidopsis tissues using microarrays Arabidopsis thaliana
24,545 RNA-Seq runs originated from 1326 NCBI SRA studies Arabidopsis thaliana
predictor was found to produce highly accurate predictions for different samples in most studies Arabidopsis thaliana
three growth-retarded lines (group 2) cluster close together in hierarchical clustering family tree
WT and ms33-6038 anther samples at stages 5–7 are closer in distance in principal-component analysis Zea mays
fruit under different temperature treatments were clearly separated by principal component analysis (PCA) Prunus persica
RNA sequencing (RNA-seq) was performed on wild type (WT) and osnam-1 Oryza sativa
(PRLIP2, AT5G24200) expression levels in the wild type were very low, so (SARD1, AT1G73805) was tested rather than (PRLIP2, AT5G24200) Arabidopsis thaliana
APX01 and (PrxIIE, AT3G52960) showed rather high expression in cotyledons
B− Myc versus NoMyc contrast shows highest number of 4514 differentially expressed transcripts Lotus japonicus
RNA extracted from roots per segregating wild type and homozygous (COI1, AT2G39940) or (AOS, CYP74A, DDE2, AT5G42650) mutants were used to construct libraries for Illumina sequencing Arabidopsis thaliana
PCA of individual genotypes revealed highly variable expression across genotypes Marchantia inflexa
different tissues and/or conditions were included to capture wide range of transcripts Amaranthus cruentus
(PRLIP2, AT5G24200) (PATHOGENESIS-RELATED LIPASE2 ) was about 50-fold more highly expressed in coi1-t than in the two wild-type lines and the (AOS, CYP74A, DDE2, AT5G42650) mutant Arabidopsis thaliana
371 genes with increased relative transcript abundance in shoots of (ATSPX4, SPX4, AT5G15330) also showed increased transcript abundance in shoots of bHLH6 OV plants Oryza sativa
456 genes with decreased relative transcript abundance in shoots of (ATSPX4, SPX4, AT5G15330) also showed decreased relative transcript levels in shoots of bHLH6 OV plants Oryza sativa
highly accurate and tissue-independent gene expression predictor can be applied universally to most Arabidopsis bulk RNA-Seq samples Arabidopsis thaliana
Enhanced expression of (ATICS1, EDS16, ICS1, SID2, AT1G74710) was also observed in coi1-1, but not in coi1-16 Arabidopsis thaliana
presence of endobacteria led to modulation of 152 genes Gigaspora margarita
eight gene modules with tissue-preferential expression derived from AtGenExpress project Arabidopsis thaliana
snRNA-seq suffer less from transcriptional artifacts
dynamically expressed genes (DYGs) were identified in Bd21, Bd3-1 and Tek-3 Brachipodium distachyon
B− Myc and B+ Myc samples partially discriminated by second principal component (PC2, y-axis) Lotus japonicus
Ca Gg presence explains 4% variance explained in plant transcriptome Lotus japonicus
60 RNAseq libraries collectively spanned ~1.3 billion reads Marchantia inflexa
8012 genes were upregulated in (EDA33, GT140, IND, IND1, AT4G00120) versus DEH samples Aethionema arabicum
genes whose expression was significantly induced (fold change >2, FDR < 0.01) in mutants compared with wild-type were selected from triplicate RNA-seq data
RNA-seq raw data were downloaded and processed via uniform purpose-built pipeline Arabidopsis thaliana
isolation of nuclei aids much broader applicability of snRNA-seq method to plant tissues
single-cell genomics enables relating genes to functions, structures, and phenotypes
bacterial genes not detected in B+ Myc samples Lotus japonicus; Candidatus Glomeribacter gigasporarum
isolation of nuclei could offer an alternative for single-nucleus RNA-sequencing (snRNA-seq)
expression pattern was independent of whether plants were mock-treated or infected Arabidopsis thaliana
(AT2G05420) was not affected by (COI1, AT2G39940) mutation Arabidopsis thaliana
(AtDOB11, AT5G54450) had expression so low that no specific PCR product was detected Arabidopsis thaliana
genes differentially expressed in coi1-t were compared to both wild types and the (AOS, CYP74A, DDE2, AT5G42650) mutant Arabidopsis thaliana
principal component analysis (PCA) examined overall variation in genome data Picea abies
single-cell transcriptome profiling enables observing changes in each cell's transcriptome and among its neighborhoods
increased expression of (ATPGMP, PGM, PGM1, STF1, AT5G51820) and (PRLIP2, AT5G24200) was confirmed in coi1-1 and the temperature-sensitive coi1-16 mutant Arabidopsis thaliana
principal component analysis (PCA) was conducted on global gene expression Marchantia inflexa
(APC1, PC1, AT5G17480) explained 66.35% of the total variance in gene expression Marchantia inflexa
baseline samples exhibited similar gene expression patterns to one another Marchantia inflexa
non-diurnal genes were expressed in more condition-specific manner than diurnally expressed genes Skeletonema robusta
24-kDa oleosin isoform down-regulated with fold change of −5.3-fold Glycine max
3 lines with insertion in peroxidase genes were chosen because of strong representation of peroxidases in cDNA library Arabidopsis thaliana
predictor model was constructed with RNA-Seq datasets available from SRA as of October 2019 Arabidopsis thaliana
spatial transcriptomics provides precise localization of mRNAs within cells of tissues
SYSTEMIC ACQUIRED RESISTANCE DEFICIENT1 (SARD1, AT1G73805) was chosen as a second gene and again found no influence of the jazD genotype Arabidopsis thaliana
RNA-sequencing (RNA-seq) was used for morph-specific sampling Aethionema arabicum
flower samples are more similar in their transcriptional profile to bud samples than to fruit samples Aethionema arabicum
quantitative PCR was used to quantify expression of three peroxidases
transcript extraction has been from homogenized amalgam of various tissues and cell types
veinal cells had an average of 13,648 transcripts detected Oryza sativa
expression was investigated in endosperm cap, non-micropylar endosperm, radicle, and cotyledons
eight WRKY genes were hubs in both susceptible and resistant accessions Brachipodium distachyon
Affymetrix soybean array underlying dataset derived from public soybean EST project Glycine max
hydrophobic seed protein precursor down-regulated with fold change of −18.7-fold Glycine max
(PRLIP2, AT5G24200) expression was not affected in 35S:JAZ1Δ3A:GUS plants Arabidopsis thaliana
presence of the AMF explains 50% variance explained in plant transcriptome Lotus japonicus
majority of genes had negative loading scores on (APC1, PC1, AT5G17480) Marchantia inflexa
replicate RNA-seq samples clustered tightly by MORPH Aethionema arabicum
16 243 genes were found to be differentially expressed in (EDA33, GT140, IND, IND1, AT4G00120) versus DEH samples Aethionema arabicum
higher level of rhythmicity of Skeletonema robusta's transcriptome might be explained by longer duration of the time series Skeletonema robusta
B− Myc versus NoMyc and B+ Myc versus NoMyc contrasts showed prevalence of downregulated genes Lotus japonicus
differential gene expression was evaluated using DESeq2 R package Lolium rigidum
computational tools for data analysis are required for comprehensive and quantitative transcript profiling
transcriptome dynamics throughout endosperm development in T. urartu were revealed using RNA-seq Triticum urartu
Lotus japonicus roots colonized by fungal line with bacteria (B+) analyzed by deep dual-mRNA sequencing Lotus japonicus; Gigaspora margarita
direct comparison B+ Myc versus B− Myc exclusive of 22 genes Lotus japonicus
transcript levels of (PRX16, AT2G18980) were significantly higher in endosperm caps than in radicles
high-throughput RNA-seq identifies non-protein-coding transcripts
down-regulated transcripts include high-proline proteins Glycine max
repetitive proline-rich protein down-regulated with fold change of −8.0-fold Glycine max
SSH-technique used to construct subtractive cDNA library
transcripts of APX01 and (PrxIIE, AT3G52960) were both already present in dry radicles and endosperm caps
nine libraries obtained from three conditions with three biological replicates each Lotus japonicus
B+ Myc versus NoMyc contrast shows 3147 differentially expressed transcripts Lotus japonicus
B− Myc versus NoMyc and B+ Myc versus NoMyc contrasts share 2447 transcripts Lotus japonicus
Handa et al. (2015) study identified 3641 DEGs Lotus japonicus; Rhizophagus irregularis
24-kDa oleosin isoform (partial) (clone P24/89) down-regulated with fold change of −3.9-fold Glycine max
Alstroemeria petal ESTs almost doubling number of ESTs reported in previously published work Alstroemeria
cDNA microarray analysed transcript profiles of Vitis vinifera cultivars Regent and Trincadeira Vitis vinifera
alternative splicing (AS) was revealed by mRNA sequencing (RNA-Seq) Phyllostachys edulis
(ATPGMP, PGM, PGM1, STF1, AT5G51820) and (PRLIP2, AT5G24200) expression was as high in coi1-t (AOS, CYP74A, DDE2, AT5G42650) as in coi1-t Arabidopsis thaliana
RNA sequencing identified differentially expressed genes (DEGs)
soybean 24-kDa oleosin isoform down-regulated with fold change of −7.5-fold Glycine max
calcium-binding EF hand protein (caleosin) up-regulated with fold change of 4.1-fold Glycine max
hydroxyproline-rich glycoprotein (sbHRGP2) mRNA, 3' end up-regulated with fold change of 3.2-fold Glycine max
84 of 229 candidates detected in previous transcriptome analysis of cotton upon V. dahliae inoculation Gossypium hirsutum
differential bri 3 transcriptome only ~30% is contained in differential (BRX, NLM9, AT1G31880) or (OPS, AT3G09070) transcriptomes Arabidopsis thaliana
At-TAX is resource for transcript identification Arabidopsis thaliana
bri 3- RESCUED transcriptome is more distant from Col-0 (n = 142; p < 0.01) than from bri 3 Arabidopsis thaliana
analysis of the gerbera floral transcriptome using EST sequencing yielded no tags for a second GGLO gene
RNA-seq analysis yielded 7–17 million reads per replicate Medicago truncatula
novel intergenic transcript units (TUs) obtained from high-throughput sequencing from control leaves (CL) and drought leaves (DL) Populus trichocarpa
transcripts from intergenic regions identified as transcript units (TUs) Populus trichocarpa
genes for stress acclimation are under-represented among upregulated genes in P-depletion treatment Medicago truncatula
RNA-Seq method has limitations in determination of full structure and strand information
28-kDa protein down-regulated with fold change of −3.0-fold Glycine max
differentially expressed genes (DEGs) include less than 30 differentially expressed transcription factors (DETFs) Marchantia polymorpha
RNA-seq analysis applied to multiple treatment samples Rorippa aquatica
each tissue-specific expression profile included most transcripts detected in any tissue (range: 77-90% of core transcripts) Panicum hallii
Gene Ontology (GO) overrepresentation analysis revealed overrepresentation of energy-demanding pathways in down-regulated genes Rorippa amphibia; Rorippa sylvestris
replicates were generally grouped together by genotype and time point Picea sitchensis
other 15% of reads contained regions of high expression within intergenic regions Populus trichocarpa
DEGs between OXmiR400 and OXrPPR1 plants include 437 significantly differentially expressed genes Arabidopsis thaliana
OXrPPR1 transgenic plants have 409 differentially expressed genes (DEGs) relative to WT plants Arabidopsis thaliana
microarray analysis provides approximately 80% genome coverage Arabidopsis thaliana
expression profile of chickpea genes in root tissue most distinct from other tissues analysed Cicer arietinum
genes exhibited preferential expression in particular tissue Cicer arietinum
genes showed preferential or specific expression in root and flower tissues Cicer arietinum
RNAseq analysis analyzed for significant transcript enrichment Arabidopsis thaliana
inclusion of outlier replicate did not impact overall statistical analyses Picea sitchensis
differentially expressed genes are defined as genes with twofold expression difference and P-value < 0.05 Oryza sativa L. ssp. Japonica
Arabidopsis (ATH1, AT4G32980) GeneChip arrays was used for microarray experiments Rorippa amphibia; Rorippa sylvestris
RNA-deep sequencing was based on genomic analysis
global expression profiles were investigated using Illumina RNA sequencing approach Oryza sativa
P-depletion nodule tissue expressed 14,330 genes Medicago truncatula
P-depletion treatment results in 1,140 differentially expressed genes Medicago truncatula
bri 3 and bri 3- RESCUED transcriptomes show even fewer differences (n = 87; p < 0.01) than between Col-0 and bri 3 Arabidopsis thaliana
Arabidopsis genome (TAIR10 annotation) is used for sequence alignment Arabidopsis thaliana
ratio of annotated exons to polyA(+) transcripts detectable on tiling arrays appears to be much higher in Arabidopsis than in some other organisms Arabidopsis thaliana
RNA sequencing (RNA-seq) performed on bri 3, bri 3- RESCUED, and Col-0 wild-type root tips Arabidopsis thaliana
genes differentially expressed between bri 3 and bri 3- RESCUED root tips only ~6% (n = 5) have been described as brassinosteroid-responsive, high-confidence (BZR1, AT1G75080) targets Arabidopsis thaliana
K-means clustering was undertaken for DEGs Raphanus sativus
mutants with reduced PRC2 activity used to profile expression of transposable elements (TEs) Cyanidioschyzon merolae; Marchantia polymorpha; Phaeodactylum tricornutum
mapping onto a reference database was chosen to overcome problem of orthology establishment assumptions
RNA-seq sequences polyadenylated RNAs
RNA sequencing reads are first assembled into transcripts Arabidopsis thaliana
nuclear RNA pool was enriched for nascent transcripts Oryza sativa
nuclear RNA and poly(A) + measures of transcript abundance yield distinct results Oryza sativa
RNA transcripts from rind tissues of internodes deep sequenced from greenhouse-grown Mo17 and (B73, CHL6, CNX, CNX1, SIR4, AT5G20990) plants Zea mays
some poly(A) + -enriched mRNAs could be those from cells that do not express the p35S Oryza sativa
chickpea lincRNAs were available for analysis with 2,248 loci Cicer arietinum
RNA-seq data generated from libraries prepared with RNA isolated from different tissues/organs Cicer arietinum
group of genes with ubiquitous expression does not significantly change based on CPM filtering Pinus pinaster
nonpolyadenylated RNAs in Arabidopsis make more limited contribution to the Arabidopsis transcriptome Arabidopsis thaliana
root tips of 7-d-old p35S:NTF2 seedlings were used for RNA-seq analysis Oryza sativa
14,264 transcripts above the 5 rpkM threshold in both populations had 6,234 significantly enriched in one or the other population (nuclear, 3,152; poly(A) + , 3,082; |log 2 fold difference| >1, FDR ≤ 0.01) Oryza sativa
genes upregulated in stone cell transcriptomes includes 1049 contigs uniquely differently expressed in R genotype Picea sitchensis
whole plants were sampled for RNA sequencing Oryza sativa L. ssp. Japonica
dormant seed indicated that its steady state pool of transcripts differed most dramatically from other tissues analyzed Sorghum bicolor
non-vernalized wild-type and ezl1-1 plants were grown to third-leaf stage and RNA isolated from entire shoot in the middle of photoperiods Brachypodium distachyon
ezl1-1 plants have nearly 1400 genes differentially expressed in relative to non-vernalized wild-type plants Brachypodium distachyon
mRNA sequencing allowed identification of 17,000 transcripts Arabidopsis thaliana
RNA-sequencing (RNA-seq) has greatly facilitated study of gene expression in non-model organisms
Remaining cultivar-specific transcripts were also transcribed from genes that varied in copy number between cultivars Vitis vinifera
expression correlation in diploid species was followed by clustering by tissue (endosperm and root)
methodology involved assembling overlapping RNA sequences (contigs), to construct Unigenes corresponding to the transcriptome of HS and NTSR plants respectively Alopecurus myosuroides
TranSeq method could efficiently discriminate between highly similar members of gene families Solanum lycopersicum
3′-end sequencing methods may be able to detect differences in expression of gene family members
sequence divergence in 3′UTR allows TranSeq to outcompete TruSeq in differentiating gene expression patterns Solanum lycopersicum
standard RNA-seq methods with sequence reads covering entire transcript has weakness of erroneous assignment of reads in-between highly related sequences such as members of same gene family
RNA sequencing was performed on seed coats harvested at 2-day intervals throughout development Cleome hassleriana
q distribution remained skewed toward maternal overrepresentation Arabidopsis thaliana
TopHat2 is used to align sequencing reads to Arabidopsis genome Arabidopsis thaliana
462 genes showed expression differences 5-fold or greater Zea mays
at least 16 transcription factors displayed 5-fold difference in expression Zea mays
portion of the transcript mapping to introns, coding regions and untranslated regions (UTRs) was evaluated in nuclear and poly(A) + RNA Oryza sativa
pollen transcriptome has been found to be most highly divergent according to MPSS (massively parallel signature sequencing of transcripts)
isolated wild-type trichomes were used for variety of analyses including preliminary transcriptome analysis using Affymetrix (ATH1, AT4G32980) GeneChip Arabidopsis thaliana
mutants with reduced PRC2 activity used to profile expression of protein-coding genes (PCGs) Cyanidioschyzon merolae; Marchantia polymorpha; Phaeodactylum tricornutum
rescue of bri 3 root phenotypes by CVP2::BRI1-CITRINE involves rather limited set of transcriptional changes Arabidopsis thaliana
rarefaction analysis of all tissues was used to estimate minimum sequencing requirements Panicum hallii
RNAs corresponding to a subset of pseudogenes are much more abundant in polyA(±) fraction Arabidopsis thaliana
filtered set of non-redundant singletons used for annotation and expression analysis
chickpea-specific genes exhibited tissue-preferential and/or stress-responsive expression 10% Cicer arietinum
tiling arrays address expression difference between two conditions
tiling arrays allow detection of all transcripts irrespective of annotation status
LOC_ genes were used for further analysis Oryza sativa
read count filtering process revealed existence of considerable number of transcripts with low expression Pinus pinaster
stage-specific transcripts were transcribed from genes located predominantly in distal chromosome regions Vitis vinifera
106 variable-shared clusters comprised 4,876 genes representing 26.9% of all modulated genes Vitis vinifera
differentially expressed genes were classified based on level of haplotype sharing between cultivars Vitis vinifera
7627 A and D subgenome homoeologs in AADD were analyzed using correlation dendrogram
cDNA libraries were prepared in biological triplicates from Peldon and Rothamsted Alopecurus myosuroides
(GL2, AT1G79840) was down-regulated in its respective mutants as compared with wild-type controls Zea mays
differential (BRX, NLM9, AT1G31880) transcriptome is nearly 90% contained in differential (OPS, AT3G09070) transcriptome Arabidopsis thaliana
expression correlation in AADD allotetraploid was followed by clustering by tissue (endosperm and root)
78 host-induced secreted proteins (SPs) identified by Tisserant et al. could confirm most 62 secreted proteins (SPs) Rhizophagus irregularis
TranSeq data provide accurate expression measurements of specific gene family members
gene family members possessing high sequence similarity can be accurately measured by TranSeq data
PC4 captured variance between sampled tissues Solanum lycopersicum
(EMA1, GIR1, SAD2, URM9, AT2G31660) OE hairy roots were compared with control hairy roots Medicago truncatula
hyperosmotic stress combined with RNA sequencing (RNA-seq) analysis Arabidopsis thaliana
cell-specific fluorescent marker lines enable analysis of transcriptome of different cell types in roots
96% of contigs detected at 0.5 million reads
tissue type had large influence on transcriptional profile clustering Sorghum bicolor
PC2, PC3 and PC4 showed similar trend between TranSeq and TruSeq methods Solanum lycopersicum
gene expression levels were stored in two matrices of nine conditions each Solanum lycopersicum
TranSeq when examining gene families, shows only one gene per family expressed to significant level while others with sequence similarity displayed much lower expression Solanum lycopersicum
all known cloned glossy genes exhibited significant DE in at least one mutant versus wild-type comparison Zea mays
principal component analysis (PCA) separated two inbred lines Raphanus sativus
leaf tissue required 10.5 million aligned reads to detect 90% of transcripts Panicum hallii
Bowtie2 is used to align sequencing reads to Arabidopsis genome Arabidopsis thaliana
Cuffnorm is used for RNA-Seq normalization Arabidopsis thaliana
Cumme(R)bund suite is used for transcriptome quality control and comparison Arabidopsis thaliana
transcriptome data assigned accession number GSE14663 Arabidopsis thaliana; Oryza sativa
plant-microbe interaction transcriptome data can be generated from single-time-point experiments
plant-microbe interaction transcriptome data can be generated from time-course experiments
KEGG pathways enriched in Experiment II (A-NA versus A-CA)
principal component analysis (PCA) clearly separated treated from control samples Rorippa amphibia; Rorippa sylvestris
S. foetida EST sequences contains 26,083 leaf EST assemblies Steculia foetida
poly(A) + RNA libraries yielded highly consistent results with R 2 ≥ 0.978, Pearson correlation Oryza sativa
23 gene models had higher expression in AI cell versus SO cells but not EAE sacs Hieracium praealtum
buds from specific rosette positions were used to conduct (ATH1, AT4G32980) microarray-based transcriptome profiling Arabidopsis thaliana
largest block of correlated expression was high correlation between all root samples regardless of whether distal or proximal or of nitrogen treatment Sorghum bicolor
set of 2 500 genes with largest sum magnitude of loadings for first three PCs were identified to identify genes with large variation in expression across dataset Sorghum bicolor
detection of differentially expressed genes (DEGs) was performed between experiments Physcomitrella patens
transcript levels were calculated as RPKM (reads per kilobase per million reads) Brassica napus
TranSeq could discriminate between transcripts that display multiple polyadenylation sites
strict Ni hyperaccumulator species with marked variation in shoot Ni content would be alternative model to identify patterns of gene expression underlying Ni hyperaccumulation
principal component analysis (PCA) profiled expression patterns of all genes Diospyros kaki
RNA-seq analysis revealed that expression of 1064 of the 41,724 expressed genes Medicago truncatula
genes identified as expressed in at least one of 16 samples Cicer arietinum
genes upregulated in stone cell transcriptomes includes 80 contigs common to upregulation in stone cells of both R and S genotypes Picea sitchensis
(APC1, PC1, AT5G17480) separated R and S genotypes Picea sitchensis
(APC1, PC1, AT5G17480) and PC2 accounted for 68.5% of the original variance Picea sitchensis
ROSMETER algorithm uses comparative approach based on vector correlation
Cuffdiff is used for differential expression analysis Arabidopsis thaliana
nuclear RNA had about 18,100 protein-coding transcripts detected Oryza sativa
transcriptomes of root cap, meristem, and elongation zone of gravistimulated wild-type and egt2 mutant roots were studied by RNA sequencing (RNA-seq) in time-course experiment Hordeum vulgare
fluorescence-activated cell sorting (FACS) is used for early attempts to increase the resolution of transcriptomics analysis
plant protoplasts is problematic as biological entities to analyze gene expression
409 DEGs in OXrPPR1 plants include 164 upregulated and 245 downregulated genes Arabidopsis thaliana
cDNA libraries were sequenced using Illumina HiSeq 4000 system Oryza sativa L. ssp. Japonica
differential expression analyses is complemented by co-expression network analyses Hordeum vulgare
genes upregulated in stone cell transcriptomes includes 164 contigs uniquely differently expressed in S genotype Picea sitchensis
RNA-seq data especially for lowly expressed isoforms challenge in obtaining reliable information
de novo transcriptome characterization strategy used to make qualitative comparisons between the cell type transcriptomes Hieracium praealtum
DEGs downregulated in OXrPPR1 are also differentially expressed but in opposite direction in OXmiR400 plants Arabidopsis thaliana
barnyard grass transcriptome yielded 278,843 transcripts and 95,223 unigenes
probe selection method based on gDNA hybridization reduces bias in transcriptome data Rorippa amphibia; Rorippa sylvestris
single-cell RNA sequencing (scRNA-seq) analysis identified fer-4 root cells exhibit a distinct clustering profile compared with wild-type roots Arabidopsis thaliana
single protoplasts isolated by glass mouth pipette yielded highly noisy RNA-seq data
marker genes of UiC2 enriched in nitrogen fixation zone (FIII) Medicago truncatula
Cufflinks determined normalized expression level as FPKM Cicer arietinum
differentially expressed genes (DEGs) between WT and ms33-6038 anthers at stages 8a–9 are significantly larger in number than DEGs at stages 5–7 Zea mays
transcriptome of S stage stands apart from transcriptomes of other developmental stages Petunia axillaris; Petunia exserta; Petunia parodii
genes differentially expressed between leaf and root Cicer arietinum
RNA-seq analysis generated 7.7–41.4 million raw reads for each sample Cucumis sativus
Col-0 and bri 3 root meristems show relatively few significant gene expression differences (n = 238; p < 0.01) Arabidopsis thaliana
MpCLE2-OX lines contain four DETFs specific to Mp (ANAC092, ATNAC2, ATNAC6, NAC2, NAC6, ORE1, AT5G39610) Mp (ANAC100, ATNAC5, NAC100, NAC5, AT5G61430) Mp (ATERF14, ERF14, ERF97, AT1G04370) and Mp ASLBD11 Marchantia polymorpha
cell-based approaches to study expression profiles by RNA-Seq need to take into account possible global shift in expression between samples
Variable-shared clusters associating cultivar, vintage and location represent part of grapevine transcriptome specifically involved in G×E interactions Vitis vinifera
negative binomial generalized linear model was used for differential expression analysis Solanum lycopersicum; Solanum pennellii
transcriptome assemblies generated by 454 sequencing of nine diverse wheat cultivars are not present in Brachypodium gene set Triticum aestivum; Brachypodium distachyon
early studies of single-cell RNA-seq in plants opened new paradigm in plant single-cell transcriptome analysis
snRNA-seq advantages come at the cost of capturing substantially less genes per cell when compared with scRNA-seq
single-cell transcriptome analysis should be used more broadly for various applications in plant biology
external phloem (EP) of five tissues has 10,660 genes (65.2%) commonly expressed Cucumis sativus
Sphagnum spp. has published transcriptome Sphagnum spp.
3′-end sequencing methods revealed that most Arabidopsis genes hold alternative polyadenylation sites Arabidopsis thaliana
original aim of this study was increase throughput of transcriptomics experiments
transcript levels were profiled in RNA pools from infected and non-infected samples Arabidopsis thaliana
gl8 was down-regulated in its respective mutants as compared with wild-type controls Zea mays
PCA and differential expression analyses revealed that same cell types from different leaf samples clustered together Arabidopsis thaliana
PCA and differential expression analyses revealed that different cell types from different leaf samples separately grouped Arabidopsis thaliana
plant single-cell transcriptome analysis studies have taken the analysis of transcriptional activity in individual cells of the Arabidopsis root to unprecedented resolution Arabidopsis thaliana
genes most highly expressed in root hair cells identified using RNA sequencing analysis Arabidopsis thaliana
31 genes were commonly upregulated in continuous external phloem (EP) system from peduncle to gynophore to fruit peripheral vascular bundle (PeVB) Cucumis sativus
approximately 81% of positive regulators identified as transcription factors have been classified as members of co-expression modules associated with increased Kranz differentiation Zea mays
RNAseq-derived transcriptomes are from sperm cells Oryza sativa ssp. japonica
transcripts with low expression ignored transcript analysis Oryza sativa
6977 transcripts have mean length of 1553 bp Oryza sativa
high-throughput sequencing technologies have enabled identification of lncRNA transcripts
TomExpress platform provides browser and integrated web tools for public RNA-Seq data visualization and data mining
167 genes were more highly expressed in infected and mock-treated coi1-t plants Arabidopsis thaliana
fungal transcripts represented 1.75% of the whole reads Lotus japonicus; Gigaspora margarita
other hydration states were less distinct in gene expression patterns Marchantia inflexa
AearMEE14 showed approximately 9-fold increase in transcript abundance (EDA33, GT140, IND, IND1, AT4G00120) flower samples Aethionema arabicum
transcriptomes of the two segregating wild types (WT coi1-t and WT (AOS, CYP74A, DDE2, AT5G42650) ) being most related, though still distinct each other Arabidopsis thaliana
119 genes upregulated in B+ fungus compared with the cured line Gigaspora margarita
1805 genes with increased relative transcript levels in bHLH6 OV lines were also upregulated in WT under low-P conditions Oryza sativa
samples from different genotypes, tissues and hydration states were broadly interspersed along (APC1, PC1, AT5G17480) Marchantia inflexa
large-scale transcriptomic data derived from broad range of tissues and conditions Arabidopsis thaliana
transcripts with sequence similarity to known transposable elements ignored transcript analysis Oryza sativa
S. foetida EST sequences contains 21,362 seed EST assemblies Steculia foetida
787 additional loci with sequence similarity to genomes of other species could correspond to unannotated noncoding transcripts Glycine max
transcriptome deep sequencing (RNA-seq) is conducted using 2-week-old seedlings of OXmiR400 and OXrPPR1 transgenic plants and WT seedlings Arabidopsis thaliana
microarray analysis revealed novel npcRNA candidates yeast; plants; Homo sapiens
5,315 non-diurnal genes showed lower expression levels than diurnally expressed genes Skeletonema robusta
long read technology enables capture of all the full length transcripts including splice variants
Venn diagrams showed the overlap for significantly differentially expressed transcript responses for (AOX1A, ATAOX1A, AtHSR3, HSR3, AT3G22370) and rpoTmp plants compared with wild-type (Col-0) plants Arabidopsis thaliana
genes for these transcripts did not overlap with the responses in the (AOX1A, ATAOX1A, AtHSR3, HSR3, AT3G22370) plants Arabidopsis thaliana
NME samples cluster closer to CAP samples Lepidium sativum
internal phloem (IP) of peduncle vascular bundle and peripheral vascular bundle (PeVB) has 64 common upregulated genes (URGs) Cucumis sativus
Modulated genes were assessed for differential expression between 2011 and 2012 vintages Vitis vinifera
4724 Unigenes varied more than two-fold between the HS and NTSR populations Alopecurus myosuroides
RNA-seq was used in global expression profiling of soybean genes in trifoliate leaves of GmGBP1-i-4 plants compared with those in wild-type plants in (SDS, AT1G14750) at flowering induction stages Glycine max
tomato genes displayed similar pattern of expression in both TruSeq and TranSeq sequencing methods Solanum lycopersicum
maternal class (q = 1) represented 13.8% of genes at globular stage Arabidopsis thaliana
inexpensive methods for profiling of the complete nuclear transcriptome developed for profiling of the complete nuclear transcriptome Oryza sativa L.
difference between these readouts was evident from weak positive correlation in abundance of RNAs in the two populations (R 0.298, Pearson correlation) Oryza sativa
50 unique gene models were identified with higher differential expression in AI cell relative to at least one of the other cell types in both mutants Hieracium praealtum
laser capture microdissection (LCM) in combination with 454 pyrosequencing, bioinformatic analyses, and in situ hybridization Hieracium praealtum
All comparisons to determine changes in transcript abundances under normal conditions were with the wild type (Col-0) Arabidopsis thaliana
high-resolution comparison of nuclear and steady-state poly(A) + transcript populations exposed distinctions in diversity and abundance of nuclear and total transcriptomes Oryza sativa L.
Total RNA-seq libraries were constructed with oligo dT-selected RNA Oryza sativa
overall transcriptome profiles were similar between the two host species Colletotrichum orbiculare
changes in transcript abundance in (AOX1A, ATAOX1A, AtHSR3, HSR3, AT3G22370) plants compared with rpoTmp plants under normal conditions compared with the wild type (Col-0) revealed that there was little in common between the two mutant lines Arabidopsis thaliana
read coverage across the transcription unit was averaged for RNAs that were significantly enriched in the nuclear or poly(A) + populations Oryza sativa
cDNA library revealed after sequencing 343 unique ESTs Medicago truncatula
K19624 line subjected to three independent hybridizations Arabidopsis thaliana
differentially expressed genes (DEGs) identified in Experiment I (F-NA versus F-CA)
RNAseq-derived transcriptomes are from vegetative cells Oryza sativa ssp. japonica
transcriptome atlas was developed with two primary goals to sample major plant organs at different developmental stages and to sample diversity of nitrogen states and sources Sorghum bicolor
single-cell RNA-Seq samples were excluded from analysis Arabidopsis thaliana
Genome browser views illustrate average transcript read distribution for BETA-GALACTOSIDASE2 (BGAL2, AT3G52840) and TRANSCRIPTION FACTOR (AtWRKY68, WRKY68, AT3G62340) Oryza sativa
M. truncatula lincRNAs were available for analysis with 5,794 loci Medicago truncatula
many genes in each QTL interval showed remarkable differences in expression fold difference Zea mays
RNA-seq analyses were performed in sulki1-8, Ler/ (ATKAS2, FAB1, KAS2, AT1G74960) NIL, and plants grown at 14°C to 16°C Arabidopsis thaliana
13 gene models had higher expression in AI cell versus EAE sacs but not SO cells Hieracium praealtum
filtered reads had mapping rate of 81.7% to 85.4% Triticum aestivum
untreated and MLD-treated wild-type microarrays still grouped closely together in principal component analysis Arabidopsis thaliana
relative expression of each gene in lower internodes 4 and 5 averaged expression levels across lower internodes Zea mays
mapping yielded average coverage of 26.7 (total [poly(A) + ] RNA) and 1.52 million (nuclear RNA) Oryza sativa
nuclear 5′-end bias was less prominent in transcripts with the highest nuclear abundance Oryza sativa
mRNA libraries were sequenced using Illumina technology Arabidopsis thaliana
genes with transcripts abundance that was significantly differentially expressed were identified with criteria P < 0.05; posterior probability of differential expression (PPDE) > 0.95; fold change > 1.5-fold Arabidopsis thaliana
antagonistic changes in transcript abundance between (AOX1A, ATAOX1A, AtHSR3, HSR3, AT3G22370) and rpoTmp were more than similarities under normal growth conditions between the two mutant lines Arabidopsis thaliana
A systematic comparison was made of nuclear RNA and poly(A) + RNA from root tips of seedlings Oryza sativa
GSEA is widely used transcriptome data interpretation tool Arabidopsis thaliana
NME samples at 13 h cluster closer to CAP samples Lepidium sativum
nuclear RNA-seq libraries were generated by rRNA subtraction and random-primer-enabled cDNA synthesis Oryza sativa
proportion of intronic to exonic reads (coding regions, 5′ UTR, 3′ UTR) was 2-fold higher in nuclear RNA in all of the biological replicates Oryza sativa
threshold of >5 reads per kilobase per million reads (rpkM) on exonic regions was applied to estimate complexity (i.e. the total number of gene transcripts detected) Oryza sativa
MapMan is widely used transcriptome data interpretation tool Arabidopsis thaliana
microarray analysis uses RNA samples Arabidopsis thaliana
NME samples cluster apart from CAP samples Lepidium sativum
in silico approaches allowed the identification of aposporous initial (AI)-enriched genes Hieracium praealtum
two conditions showed clear variation between expression profiles Triticum aestivum
number of DEGs at each time point is similar between Koshihikari and Takanari Oryza sativa
rice cultures exposed to cyprosulfamide had transcriptome changes determined by RNA-seq analysis
RNA-seq approaches were initially used in Chlamydomonas reinhardtii Chlamydomonas reinhardtii
nuclear RNA library sequencing identified over 7000 lncRNAs Oryza sativa
80% reads were mapped to current soybean reference genome assembly Glycine max
TranSeq experiment requires as little as 1–2 million reads per sample to cover majority of tomato transcriptome Solanum lycopersicum
1064 genes with significantly altered expression was significantly altered in (EMA1, GIR1, SAD2, URM9, AT2G31660) OE lines Medicago truncatula
Arabidopsis thaliana roots were sampled for RNA sequencing analysis Arabidopsis thaliana
principal component analysis was performed on global structure of the transcriptome dataset Arabidopsis thaliana
4482 flower DEGs were regulated at least 2-fold between DEH and (EDA33, GT140, IND, IND1, AT4G00120) Aethionema arabicum
Gene Ontology (GO) terms associated with up- and downregulated transcripts Aethionema arabicum
deep RNA-sequencing (RNA-seq) performed on B+ Myc and B− Myc Lotus japonicus roots Lotus japonicus
snRNA-seq has broader applicability to plant tissues compared to scRNA-seq
14,264 transcripts were shared by both RNA populations Oryza sativa
14 gene models had higher expression in AI cell versus both SO cells and EAE sacs Hieracium praealtum
75 stage-specific clusters comprised 6,793 genes accounting for 37.5% of all modulated genes Vitis vinifera
Vintage and location variables were associated with 39 clusters and 1,478 genes Vitis vinifera
PCA revealed striking difference in gene expression clusters between Pantoea deleyi SH-355-colonization and control groups
methodology opens way to analyze transcriptomic data from tissues dissected from tomato fruit Solanum lycopersicum
high-throughput RNA sequencing (RNA-seq) is method of choice to define and analyze transcriptomes
Loci homozygous in Cabernet Sauvignon and heterozygous in Sangiovese were overrepresented in clusters of transcripts explaining G×E interactions Vitis vinifera
expression correlation in AADD allotetraploid was first clustered by subgenome (AlloA and AlloD)
TranSeq method detected 17,854 genes Solanum lycopersicum
TranSeq reads originating from 3′-ends of transcripts is probably due to increased sensitivity for recent duplicates Solanum lycopersicum
wild-type (WT) Col-0 and (AT-PHH1, ATCRY2, CRY2, FHA, PHH1, AT1G04400) null-mutant seedlings were compared by RNA sequencing (RNA-seq) Arabidopsis thaliana
deep-sequencing studies have been conducted on gamete transcriptomes
TomExpress is fully dedicated to processing tomato RNA-Seq data Solanum lycopersicum
difference was due to both distinctions in transcriptome complexity and transcript abundance Oryza sativa
genes with significantly increased fold change in AI cell relative to EAE sacs and SO cell type transcriptomes were compared with differential gene lists from comparisons between whole ovary transcriptomes of apomict R35 and apospory-deficient mutants m115 and m134 Hieracium praealtum
RNA-seq reads mapped to chickpea genome (kabuli, v1.0) Cicer arietinum
9,821 genes accounts for 42.2% of annotated genes in cucumber genome Cucumis sativus
poly(A)− RNA library sequencing identified over 7000 lncRNAs Oryza sativa
cDNA libraries from Peldon and Rothamsted subjected to global RNA-Seq analysis using the IonTorrent sequencing platform Alopecurus myosuroides
expressed secreted proteins (SPs) were included with minimal read count of 100 for combined replicates Rhizophagus irregularis
RNA-seq broadened use from model organisms to numerous other organisms
PC3 captured variance between sampled tissues Solanum lycopersicum
TruSeq method could not detect gene expression in ORTHO000275_2 group Solanum lycopersicum
rest of gene families showed no significant difference in detection of gene expression between TranSeq and TruSeq Solanum lycopersicum
TranSeq method revealed that Solyc07g064130 was highly expressed while Solyc10g006480 and Solyc11g005670 displayed lower expression Solanum lycopersicum
novel methodologies to study gene expression diversity should deal with larger sample sets and minute amounts of RNA per sample
use of nuclear RNAs does not introduce major bias for gene expression studies
library containing 3′-end of all polyadenylated RNA molecules includes micro-RNAs (miRNA)
altered pattern of transcriptome in the root is remarkably different from root hair Zea mays
next-generation sequencing becomes challenging to obtain reliable information on spliced isoforms from RNA-Seq data alone
differentially expressed genes between stone cells and cortical parenchyma revealed 244 transcripts significantly upregulated in stone cells Picea sitchensis
gDNA hybridization signal threshold of 80 retains 97% of probe sets Rorippa amphibia; Rorippa sylvestris
220 putative effectors predicted by Sędzielewska Toro and Brachmann could only confirm 43 secreted proteins (SPs) Rhizophagus irregularis
CR-lncRNA1459-21-1 mutant has 3379 upregulated DEGs and 1584 downregulated DEGs Solanum lycopersicum
TruSeq method was more sensitive and outcompeted TranSeq in absolute numbers of detected duplicates Solanum lycopersicum
marker genes of UiC1 and UiC2 enriched in un-infected cells localized in fixation zone Medicago truncatula
late ABA-responsive factor (factor 5) is present in cluster 5 Talinum triangulare
gene ontology (GO) terms related to meristem development, cell growth, anatomical structure morphogenesis/development, macromolecule or primary or secondary metabolic process, defense response and trichoblast differentiation were highly enriched in upregulated genes (URGs) in peripheral vascular bundle (PeVB) Cucumis sativus
Bryum argenteum has published transcriptome Bryum argenteum
Pellia endiviifolia has published transcriptome dataset Pellia endiviifolia
outer cotyledon (OC) and inner cotyledon (IC) could not be separated in principal component analysis Brassica napus
TranSeq generates reads matching 3′UTRs of transcripts
top 50 marker genes from each cluster screened in different tissues/zones of 15-dpi and 21-dpi nodules Medicago truncatula
3478 genes were highly expressed under –Fe conditions Triticum aestivum