GEO DataSets

(Submitter supplied) Paired End PolyA-+ RNA-sequencing of NGP cells with and without NGP treatment in 10 replicates.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

20 Samples

Download data: TSV

(Submitter supplied) RNA-sequencing was used to screen all differentially expressed (DE) lncRNAs and mRNAs between the RSD and control groups. In mice experiencing RSD, 373 and 454 lncRNAs, along with 1142 and 654 mRNAs were significantly upregulated and downregulated, respectively.Available informatics evidence highlighted the likely role of synapse dysfunction and abnormal synaptic neurotransmission in these behaviors. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

6 Samples

Download data: XLSX

(Submitter supplied) Long non-coding RNA (lncRNA) have been implicated in human pathology, however, their roles in colorectal carcinogenesis has not been fully elucidated. In the current study, whole-transcriptome was analyzed in 3 pairs of colorectal cancer (CRC) and matched normal mucosa (NM) by RNA sequencing (RNA-seq). Followed by confirmation using the Cancer Genome Atlas (TCGA) dataset, we identified 27 up-regulated and 22 down-regulated lncRNAs in CRC. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: CSV

(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) We performed a genome-wide analysis of lncRNA expression to identify novel targets for the further study of liver metastasis in CRC. Samples obtained from CRC patients were analyzed using Arraystar human 8×60K lncRNA/mRNA v3.0 microarrays chips to find differentially expressed lncRNAs and mRNAs; The results were confirmed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The differentially expressed lncRNAs and mRNAs were identified through fold-change filtering. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL16956

12 Samples

Download data: TXT

(Submitter supplied) We report the altered expression profiles of lncRNA and mRNA in mice cortex afetr traumatic brain injury (TBI).Total of 27,457 transcripts were identified as mRNA and 37,073 transcripts were identified as lncRNA. Total of 823 lncRNAs and 1,580 mRNAs were significantly changed after TBI according to the criteria: |log2(fold change)|>1, P<0.05. In addition, total of 360 new mRNAs and 8,041 new lncRNAs were identified in current sequencing study.

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: XLS

(Submitter supplied) As part of functional characterization of neuroblastoma associated lncRNA HOXD-AS1, we performed its knock-down in neuroblastoma cell line SH-SY5Y, which resulted in modulation of expression levels of a set of genes involved in angiogenesis and inflammation, the hallmarks of metastatic cancer.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL19057

142 Samples

Download data

(Submitter supplied) The advent of Next Generation Sequencing has allowed transcriptomes to be profiled with unprecedented accuracy, but the steep costs associated with full-length library sequencing have posed a limit on the accessibility and scalability of the technology. To address these limitations, we developed 3’Pool-seq, a simple, cost-effective, and scalable RNA-seq method that focuses sequencing to the 3’ end of mRNA transcripts.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

80 Samples

Download data: TXT

(Submitter supplied) The advent of Next Generation Sequencing has allowed transcriptomes to be profiled with unprecedented accuracy, but the steep costs associated with full-length library sequencing have posed a limit on the accessibility and scalability of the technology. To address these limitations, we developed 3’Pool-seq, a simple, cost-effective, and scalable RNA-seq method that focuses sequencing to the 3’ end of mRNA transcripts.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

32 Samples

Download data: TXT

(Submitter supplied) The advent of Next Generation Sequencing has allowed transcriptomes to be profiled with unprecedented accuracy, but the steep costs associated with full-length library sequencing have posed a limit on the accessibility and scalability of the technology. To address these limitations, we developed 3’Pool-seq, a simple, cost-effective, and scalable RNA-seq method that focuses sequencing to the 3’ end of mRNA transcripts.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

24 Samples

Download data: TXT

(Submitter supplied) The advent of Next Generation Sequencing has allowed transcriptomes to be profiled with unprecedented accuracy, but the steep costs associated with full-length library sequencing have posed a limit on the accessibility and scalability of the technology. To address these limitations, we developed 3’Pool-seq, a simple, cost-effective, and scalable RNA-seq method that focuses sequencing to the 3’ end of mRNA transcripts.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: TXT

(Submitter supplied) Motivation: RNA-seq is replacing microarrays as the primary tool for gene expression studies. Many RNA-seq studies have used insufficient biological replicates, resulting in low statistical power and inefficient use of sequencing resources. Results: We show the explicit trade-off between more biological replicates and deeper sequencing in increasing power to detect differentially expressed (DE) genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

14 Samples

Download data: TXT

(Submitter supplied) The EZH2 histone methyltransferase is highly expressed in germinal center (GC) B-cells and targeted by somatic mutations in B-cell lymphomas. Here we find that EZH2 deletion or pharmacologic inhibition suppresses GC formation and functions in mice. EZH2 represses proliferation checkpoint genes and helps establish bivalent chromatin domains at key regulatory loci to transiently suppress GC B-cell differentiation. more...

Organism:

Mus musculus; Homo sapiens

Type:

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

Platforms:

GPL13112 GPL11154 GPL10999

61 Samples

Download data: BED, TXT, WIG

(Submitter supplied) BCL6 is crucial for B-cell activation and lymphomagenesis. We used integrative genomics to explore BCL6 mechanism in normal and malignant B-cells. Surprisingly, BCL6 assembled distinct complexes at enhancers vs. promoters. At enhancers BCL6 preferentially recruited SMRT, which mediated H3K27 deacetylation through HDAC3, antagonized p300 activity and repressed transcription, but without decommissioning enhancers. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL15433 GPL10999 GPL11154

46 Samples

Download data: BED, BW, TXT, WIG

(Submitter supplied) We identified 13,072 mRNAs and 19,129 lncRNAs, of which 2,977 mRNAs and 1,527 lncRNAs were differential expressed in pigeon BFs over three developmental stages.

Organism:

Columba livia

Type:

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

Platform:

GPL29485

9 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL21103 GPL17021

30 Samples

Download data

(Submitter supplied) The goals of this study are to explore the differential expression of non-coding RNAs in mice kidne during aging

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17021

15 Samples

Download data: TXT

(Submitter supplied) The goals of this study are to explore the differential expression of non-coding RNAs in mice kideny during aging

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21103

15 Samples

Download data: TXT

(Submitter supplied) Recent advances in transcriptome sequencing have enabled the discovery of thousands of long non-coding RNAs (lncRNAs) across many species. Though several lncRNAs have been shown to play important roles in diverse biological processes, the functions and mechanisms of most lncRNAs remain unknown. Two significant obstacles lie between transcriptome sequencing and functional characterization of lncRNAs: identifying truly non-coding genes from de novo reconstructed transcriptomes, and prioritizing the hundreds of resulting putative lncRNAs for downstream experimental interrogation. more...

Organism:

Mus musculus; Homo sapiens; Mus musculus castaneus; Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

9 Samples

Download data: TXT, WIG