rna-seq - GEO DataSets

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Results: 1 to 20 of 2758

Select item 2000412651.

Single-cell transcriptomics reveals widespread heterogeneity in gene regulation and RNA processing in stimulated immune cells

(Submitter supplied) Here, we used single-cell RNA-Seq to discover extensive cell-to-cell variability – in transcript expression levels, cell state, circuit usage, and alternative splicing – between stimulated immune cells

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13112
24 Samples

Download data:: GEO (TXT), SRA SRP015959

Series

Accession:: GSE41265

ID:: 200041265

Select item 2000462072.

Impairment of Muscle Regeneration in Muscleblind-like 3 Isoform Knockout Mice

(Submitter supplied) We have performed an RNA-seq experiment to identify expression and alternative splicing differences between WT and Mbnl3 isoform knockout mice E15 forelimbs. We have also identified and characterized transcriptome wide Mbnl3-binding sites in C2C12 cells and E15 forelimbs.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL11002
15 Samples

Download data:: GEO (BED, BEDGRAPH, TXT, XLS), SRA SRP021195

Series

Accession:: GSE46207

ID:: 200046207

Analyze with GEO2R

Select item 2000454283.

Using RNA-Seq to create sample-specific proteomic databases that enable mass spectrometric discovery of splice junction peptides

(Submitter supplied) Many new alternative splice forms have been detected at the transcript level using next generation sequencing (NGS) methods, especially RNA-Seq, but it is not known how many of these transcripts are being translated. Leveraging the unprecedented capabilities of NGS, we collected RNA-Seq and proteomics data from the same cell population (Jurkat cells) and created a bioinformatics pipeline that builds customized databases for the discovery of novel splice-junction peptides. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
3 Samples

Download data:: GEO (BED, TXT), SRA SRP019939

Series

Accession:: GSE45428

ID:: 200045428

Select item 2000470104.

Clostridium thermocellum ATCC27405 Transcriptomic Profiles during growth on Populus and switchgrass

(Submitter supplied) The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. It expresses enzymes for both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. To gain insights into the C. thermocellum genes, using an updated version of the C. thermocellum ATCC 27405 genome annotation, that are required for specific growth on the cellulosic feedstocks of either pretreated switchgrass or Populus, duplicate fermentations were conducted with a 5 g/L solid substrate loading. more...

Organism:: Clostridium thermocellum ATCC 27405; Clostridium thermocellum 27405

Type:: Expression profiling by array

Platform:: GPL17171
8 Samples

Download data:: GEO (CALLS, PAIR)

Series

Accession:: GSE47010

ID:: 200047010

Analyze with GEO2R

Select item 2000469155.

Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution

(Submitter supplied) We used deep RNA sequencing to obtain high coverage RNA-Seq data of five C. crescentus cell cycle stages, each with three biological replicates. We found that 1,586 genes (over a third of the genome) display significant differential expression between stages. This gene list, which contains many genes previously unknown for their cell cycle regulation, includes almost half of the genes involved in primary metabolism, suggesting that these "house-keeping" genes are not constitutively transcribed during the cell cycle, as often assumed. more...

Organism:: Caulobacter vibrioides

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17158
15 Samples

Download data:: GEO (CSV), SRA SRP022592

Series

Accession:: GSE46915

ID:: 200046915

Select item 2000407056.

Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples

(Submitter supplied) RNA-Seq is an effective method to study the transcriptome, but can be difficult to apply to scarce or degraded RNA from fixed clinical samples, rare cell populations, or cadavers. Recent studies have proposed several methods for RNA-Seq of low quality and/or low quantity samples, but their relative merits have not been systematically analyzed. Here, we compare five such methods using a comprehensive set of metrics, relevant to applications such as transcriptome annotation, transcript discovery, and gene expression. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL11154 GPL16791
18 Samples

Download data:: GEO (TXT), SRA SRP015640

Series

Accession:: GSE40705

ID:: 200040705

Select item 2000409967.

Steroid-induced changes in gene expression of airway smooth muscle in patients with asthma

(Submitter supplied) Rationale: Steroids are the mainstay of asthma therapy. However, it is unclear whether the benefits of steroids in asthma are merely based on anti-inflammatory properties. Steroids may also alter gene expression of airway smooth muscle (ASM). Hypothesis and Aims: We hypothesized that the transcriptomic profile of the ASM layer in endobronchial biopsies of atopic asthma patients changes by oral steroid therapy. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL14603
24 Samples

Download data:: GEO (CSV), SRA SRP015815

Series

Accession:: GSE40996

ID:: 200040996

Select item 2000371848.

Dynamic binding of RBPJ is determined by Notch signalling status

(Submitter supplied) Notch signalling plays crucial roles in mediating cell fate choices in all metazoans largely by specifying the transcriptional output of one cell in response to a neighbouring cell. The DNA-binding protein RBPJ is the principle effector of this pathway in mammals and together with the transcription factor moiety of Notch (NICD) it regulates the expression of target genes. The prevalent view presumes that RBPJ statically occupies consensus binding sites while exchanging repressors for activators in response to NICD. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:: GPL13112 GPL11002
33 Samples

Download data:: GEO (BED, RPKM, WIG), SRA SRP012155

Series

Accession:: GSE37184

ID:: 200037184

PubMed Similar studies

Select item 2000461009.

A transcriptome-wide RNAi screen in the Drosophila ovary reveals factors of the germline piRNA pathway [RNA-Seq]

(Submitter supplied) The Drosophila piRNA pathway provides an RNA-based immune system that defends the germline genome against selfish genetic elements. Two inter-related branches of the piRNA system exist: somatic cells that support oogenesis only employ Piwi, whereas germ cells utilize a more elaborated pathway centered on the three gonad-specific Argonaute proteins Piwi, Aubergine, and Argonaute3. While several key factors of each branch have been identified, our current knowledge is insufficient to explain the complex workings of the piRNA machinery. more...

Organism:: Drosophila melanogaster

Type:: Expression profiling by high throughput sequencing

Platform:: GPL13304
28 Samples

Download data:: GEO (TXT), SRA SRP021103

Series

Accession:: GSE46100

ID:: 200046100

Select item 20004681010.

Nucleotide-resolution, genome-wide, 5'-end maps of the transcriptome of Propionibacterium acnes (cultured with and without potassium downshift)

(Submitter supplied) The differential RNA-seq data contained within this entry is complemented by global RNA-seq and microarray data, which is also deposited in GEO.

Organism:: Propionibacterium acnes KPA171202

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17147
4 Samples

Download data:: GEO (TXT), SRA SRP022251

Series

Accession:: GSE46810

ID:: 200046810

Select item 20003776511.

A high dimensional deep sequencing study of non-small cell lung adenocarcinoma in never-smoker Korean females

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Homo sapiens

Type:: Genome variation profiling by array; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:: GPL10153 GPL10999
48 Samples

Download data:: GEO (TXT)

Series

Accession:: GSE37765

ID:: 200037765

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20003776412.

A high dimensional deep sequencing study of non-small cell lung adenocarcinoma in never-smoker Korean females [Seq]

(Submitter supplied) One of the most fertile applications of next generation sequencing will be in the field of cancer genomics. Here, we report a high-throughput multi-dimensional sequencing study of primary non-small cell lung adenocarcinoma tumors and adjacent normal tissues of 6 never-smoker Korean female patients. Our data encompass results from exome-seq, RNA-seq, small RNA-seq, and MeDIP-seq. We identified and validated novel genetic aberrations including 47 somatic mutations and 20 fusion transcripts. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:: GPL10999
36 Samples

Download data:: GEO (TXT, XLSX), SRA SRP012656

Series

Accession:: GSE37764

ID:: 200037764

PubMed Full text in PMC Similar studies

Select item 20003775913.

A high dimensional deep sequencing study of non-small cell lung adenocarcinoma in never-smoker Korean females [aCGH]

Organism:: Homo sapiens

Type:: Genome variation profiling by array

Platform:: GPL10153
12 Samples

Download data:: GEO (TXT)

Series

Accession:: GSE37759

ID:: 200037759

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20004600914.

A genome-wide RNAi screen draws a genetic framework for transposon control and primary piRNA biogenesis in Drosophila

(Submitter supplied) A large fraction of our genome consists of mobile genetic elements. Governing transposons in germ cells is critically important, and failure to do so compromises genome integrity, leading to sterility. In animals, the piRNA pathway is the key to transposon constraint, yet the precise molecular details of how piRNAs are formed and how the pathway represses mobile elements remain poorly understood. In an effort to identify general requirements for transposon control and novel components of the piRNA pathway, we carried out a genome-wide RNAi screen in Drosophila ovarian somatic sheet cells. more...

Organism:: Drosophila melanogaster

Type:: Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:: GPL9061 GPL13304
37 Samples

Download data:: GEO (BED, TXT), SRA SRP021026

Series

Accession:: GSE46009

ID:: 200046009

Select item 20004551715.

SR Proteins Collaborate with 7SK and Promoter-Associated Nascent RNA to Release Paused Polymerase

(Submitter supplied) RNAP II is frequently paused near gene promoters in mammals and its transition to productive elongation requires active recruitment of P-TEFb, a cyclin-dependent kinase for RNAP II and other key transcription elongation factors. A fraction of P-TEFb is sequestered in an inhibitory complex containing the 7SK noncoding RNA, but it has been unclear how P-TEFb is switched from the 7SK complex to RNAP II during transcription activation. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other

Platforms:: GPL9250 GPL13112
30 Samples

Download data:: GEO (BIGWIG), SRA SRP020006

Series

Accession:: GSE45517

ID:: 200045517

Select item 20004366616.

Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing

(Submitter supplied) Background: In recent years, a variety of small RNAs derived from other RNAs with well-known functions such as tRNAs and snoRNAs, have been identified. The functional relevance of these RNAs is largely unknown. To gain insight into the complexity of snoRNA processing and the functional relevance of snoRNA-derived small RNAs, we sequenced long and short RNAs, small RNAs that co-precipitate with the Argonaute 2 protein and RNA fragments obtained in photoreactive nucleotide-enhanced crosslinking and immunoprecipitation (PAR-CLIP) of core snoRNA-associated proteins. more...

Organism:: Homo sapiens

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

Platform:: GPL11154
10 Samples

Download data:: GEO (BED), SRA SRP018104

Series

Accession:: GSE43666

ID:: 200043666

Select item 20004670017.

AID stabilizes a stem cell phenotype by removing epigenetic memory of secondary pluripotency network genes

(Submitter supplied) The activation-induced cytidine deaminase enzyme (AID) is required in germinal center (GC) B cells for somatic hyper-mutation and class switch recombination at the immunoglobulin locus. In GC-B cells, AID is highly expressed, with inherent mutator activity that helps generate antibody diversity. However, AID may also regulate gene expression epigenetically, irrespective of mutator activity, by directly deaminating 5-methylcytosine (5mC) in concert with base excision repair glycosylases to exchange unmethylated cytosine. more...

Organism:: Mus musculus

Type:: Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:: GPL13112
14 Samples

Download data:: GEO (TXT), SRA SRP022150

Series

Accession:: GSE46700

ID:: 200046700

Select item 20004666918.

A Snapshot of the Hepatic Transcriptome: Ad Libitum Alcohol Intake Suppresses Expression of Cholesterol Synthesis Genes in Alcohol-Preferring (P) Rats

(Submitter supplied) Introduction: Though heavy alcohol drinking has been well characterized as causing a variety of injuries, recent epidemiological evidence in humans suggests moderate consumption may provide beneficial effects. For example, there exists a J- or U-shaped relationship between the level of alcohol intake and cardiovascular disease risk. We investigated the underlying mechanisms of these positive consequences by identifying which genes are responsive to moderate alcohol intake in the liver, the primary site for alcohol metabolism. more...

Organism:: Rattus norvegicus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17116
12 Samples

Download data:: GEO (TXT), SRA SRP022136

Series

Accession:: GSE46669

ID:: 200046669

Select item 20004471819.

Multiple roles for Grainyheadlike transcription factors in the establishment and maintenance of human mucociliary airway epithelium

(Submitter supplied) The airways of the human lung are lined by an epithelium made up of ciliated and secretory luminal cells and undifferentiated p63+ Krt5+ basal cells. The integrity of this epithelium and its ability to act as a selective barrier are critical for normal lung function. In other epithelia there is evidence that transcription factors of the evolutionarily conserved grainyheadlike (GRHL) family play key roles in co-ordinating the expression of numerous proteins required for epithelial morphogenesis, differentiation, remodeling and repair. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
8 Samples

Download data:: GEO (TAB), SRA SRP018883

Series

Accession:: GSE44718

ID:: 200044718

Select item 20004619420.

Multiple roles for Grainyhead-like transcription factors in the establishment and maintenance of human mucociliary airway epithelium (ChIP-Seq)

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL11154
6 Samples

Download data:: GEO (BEDGRAPH), SRA SRP021180

Series

Accession:: GSE46194

ID:: 200046194

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