GEO DataSets

(Submitter supplied) In this study, we aim to present a global view of transcriptome dynamics in different tissues/organs/developmental stage in chickpea. We generated about ~31-95 million reads from each of 94 libraries representing 32 different tissues/organs using Illumina platform. We generated a hybrid assembly of these data along with PacBio data to produce full-length transcriptome assembly. We mapped the reads to the transcriptome assembly for estimation of the abundance of coding and long non-coding transcripts in different tissue samples. more...

Organism:

Cicer arietinum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20619

32 Samples

Download data: FA, TXT

(Submitter supplied) In this study, we aim to present a global view of transcriptome dynamics during flower development in chickpea. We generated around 234 million high-quality reads for eight flower development stages (ranging from 16 to 40 million reads for each stage) and 91 million high-quality reads from three vegetative tissues using Illumina high-throughput sequencing GAII platform. Because of non-availability of reference genome sequence, we mapped the reads to chickpea transcriptome comprised of 34,760 transcripts for estimation of their transcriptional activity in different tissue samples. more...

Organism:

Cicer arietinum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16348

11 Samples

Download data: TXT

(Submitter supplied) This study aimed to quantify and compare the mRNA abundance of all major XPGs in liver and intestine between conventional (CV) and germ-free (GF) mice using RNA-Seq. The CV RNA-Seq data were previously uploaded to GEO database by the same research group (GSE79848). All CV and GF mice were age-matched, and were analyzed under the same conditions (diet, water, bedding, and animal facility).

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

33 Samples

Download data: ZIP

(Submitter supplied) This study aimed to quantify and compare the mRNA abundance of all major XPGs in liver and intestine using RNA-Seq. The mRNA profiles of 304 XPGs, including phase-I, phase-II enzymes, phase-II cosubstrate synthetic enzymes, xenobiotic transporters, as well as xenobiotic-related transcription factors, were systematically examined in liver and various sections of the intestine in adult male C57BL/6J mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

15 Samples

Download data: BEDGRAPH, XLS

(Submitter supplied) Transcriptome of human retinal endothelial cells (hRECs) treated with low glucose (LG), high glucose (HG) or high glucose with 4 uM TTR (HG+TTR) were conducted. Differentially expressed lncRNAs, mRNAs and TTR related lncRNAs and mRNA were acquired for further analysis. Functional annotation and enrichment including KEGG pathway, GO and GSEA were applied to analyze TTR regulated pathway and process. WGCNA analysis was implemented to obtain hub modules and genes. LncRNA-mRNA regulatory network were constructed based on cis, trans and ceRNA acting mode.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

9 Samples

Download data: TXT

(Submitter supplied) Background The combination of high-throughput transcript profiling and next-generation sequencing technologies is a prerequisite for genome-wide comprehensive transcriptome analysis. Our recent innovation of deepSuperSAGE is based on an advanced SuperSAGE protocol and its combination with massively parallel pyrosequencing on Roche’s 454 sequencing platform. As a demonstration of the power of this combination, we have chosen the salt stress transcriptomes of roots and nodules of the third most important legume crop chickpea (Cicer arietinum L.). more...

Organism:

Cicer arietinum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11675

4 Samples

Download data

(Submitter supplied) Recent discovery that much of the mammalian genome does not encode protein-coding genes (PCGs) has brought widespread attention to long noncoding RNAs (lncRNAs) as a novel layer of biological regulation. Enhancer lnc (elnc) RNAs from the enhancer regions of the genome carry the capacity to regulate PCGs in cis or in trans. Spotted fever rickettsioses represent the consequence of host infection with Gram-negative, obligate intracellular bacteria in the Genus Rickettsia. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18480

6 Samples

Download data: XLSX

(Submitter supplied) In this study, by transcriptome-wide approach we demonstrate that lncRNAs are prevalent in CCMs disease and are likely to play critical roles in regulating important signaling pathways involved in the disease progression. We believe, that detailed future investigations on these set of identified lncRNAs can provide useful insights into the biology and, ultimately, in preventing this debilitating disease.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

14 Samples

Download data: TXT

(Submitter supplied) Intronic and intergenic long noncoding RNAs (lncRNAs) are emerging gene expression regulators. The molecular pathogenesis of renal cell carcinoma (RCC) is still poorly understood, and in particular, limited studies are available for intronic lncRNAs expressed in RCC. Microarray experiments were performed with two different custom-designed arrays enriched with probes for lncRNAs mapping to intronic genomic regions. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array; Expression profiling by array

Platforms:

GPL4051 GPL3985

80 Samples

Download data: TXT

(Submitter supplied) Intronic and intergenic long noncoding RNAs (lncRNAs) are emerging gene expression regulators. The molecular pathogenesis of renal cell carcinoma (RCC) is still poorly understood, and in particular, limited studies are available for intronic lncRNAs expressed in RCC. Microarray experiments were performed with two different custom-designed arrays enriched with probes for lncRNAs mapping to intronic genomic regions. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array; Expression profiling by array

Platform:

GPL4051

4 Samples

Download data: TXT

(Submitter supplied) Intronic and intergenic long noncoding RNAs (lncRNAs) are emerging gene expression regulators. The molecular pathogenesis of renal cell carcinoma (RCC) is still poorly understood, and in particular, limited studies are available for intronic lncRNAs expressed in RCC. Microarray experiments were performed with two different custom-designed arrays enriched with probes for lncRNAs mapping to intronic genomic regions. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array; Expression profiling by array

Platform:

GPL3985

32 Samples

Download data: TXT

(Submitter supplied) Intronic and intergenic long noncoding RNAs (lncRNAs) are emerging gene expression regulators. The molecular pathogenesis of renal cell carcinoma (RCC) is still poorly understood, and in particular, limited studies are available for intronic lncRNAs expressed in RCC. Microarray experiments were performed with two different custom-designed arrays enriched with probes for lncRNAs mapping to intronic genomic regions. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array; Expression profiling by array

Platform:

GPL3985

44 Samples

Download data: TXT

(Submitter supplied) In this study, we sequenced small RNA content from seven major tissues/organs employing Illumina technology. More than 154 million reads were generated using Illumina high-throughput sequencing GAII platform, which represented more than 20 million distinct small RNA sequences. After pre-processing, several conserved and novel miRNAs were identified in chickpea. Further, the putative targets of chickpea miRNAs were identified and their functional categorization was analyzed. more...

Organism:

Cicer arietinum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16348

7 Samples

Download data: FA

(Submitter supplied) In this study, we aim to present a global view of transcriptome dynamics during salinity stress in different chickpea genotypes. We generated about 600 million high-quality reads from 16 libraries (control and stress samples for two chickpea genotypes for salinity stress at two developmental stages) using Illumina high-throughput sequencing platform. We mapped the reads to the kabuli chickpea genome for estimation of their transcript abundance in different tissue samples. more...

Organism:

Cicer arietinum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20619

8 Samples

Download data: TXT

(Submitter supplied) In this study, we aim to present a global view of transcriptome dynamics during drought stress in different chickpea genotypes. We generated about 800 million high-quality reads from 14 libraries (control and stress samples for two chickpea genotypes for drought stress at two developmental stages) using Illumina high-throughput sequencing platform. We mapped the reads to the kabuli chickpea genome for estimation of their transcript abundance in different tissue samples. more...

Organism:

Cicer arietinum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20619

8 Samples

Download data: TXT

(Submitter supplied) Cryptocaryonosis caused by Cryptocaryon irritans is one of the major diseases of large yellow croaker (Larimichthys crocea), which lead to massive economic losses annually. The pathogenesis for cryptocaryonosis has been researched by a series of transcriptome studies under different infection conditions. However, little is known about the roles of tissue-specifically expressed genes during the infection of C. more...

Organism:

Larimichthys crocea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30112

15 Samples

Download data: TXT

(Submitter supplied) We present the NEUTRA database, a catalogue of the Neurospora transcriptome, based on RNA-Seq, RNAPII ChIP-Seq and ribosome fractionation studies. The database also includes genome-wide binding sites of transcription factors involved in regulation of circadian gene expression. In a comprehensive analysis of the transcriptome we identified and characterized 1478 long intergenic non-coding RNAs (lincRNAs) and 1056 natural antisense transcripts. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL16164 GPL20705 GPL17918

8 Samples

Download data: BIGWIG, TXT

(Submitter supplied) We describe a total 222.19 Gb of pig RNA-seq sequences generated from the 18 libraries

Organism:

Sus scrofa; Sus scrofa domesticus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL24207 GPL22918

18 Samples

Download data: TXT

(Submitter supplied) In this study, we used RNA-sequencing to profile the long non-coding RNA (lncRNA) transcriptome in lesional skin from psoriasis patients before (PP) and after treatment (PT) with adalimumab and in normal skin from healthy individuals (NN). For this we sequenced total RNA from 18 psoriasis patients (before and after treatment) and 16 healthy controls. We created our own reference set of long non-coding RNAs by merging three long non-coding RNA reference data sets. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

52 Samples

Download data: TXT

(Submitter supplied) Background: As core units of organ tissues, cells of various types play their harmonious rhythms to maintain the homeostasis of the human body. It is essential to identify the characteristics of cells in human organs and their regulatory networks for understanding the biological mechanisms related to health and disease. However, a systematic and comprehensive single-cell transcriptional profile across multiple organs of a normal human adult is missing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20795

45 Samples

Download data: CSV