Similar studies for GEO DataSets (Select 200069506) - GEO DataSets

(Submitter supplied) While long noncoding RNAs (lncRNAs) and mRNAs share similar biogenesis pathways, these two transcript classes differ in many regards. LncRNAs are less conserved, less abundant, and more tissue specific than mRNAs, implying that our understanding of lncRNA transcriptional regulation is incomplete. Here, we perform an in depth characterization of numerous factors contributing to this regulation. We find that lncRNA promoters contain fewer transcription factor binding sites than do those of mRNAs, with some notable exceptions. more...

Organism:: Homo sapiens

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

Platform:: GPL16791
30 Samples

Download data: TXT

Series

Accession:: GSE80045

ID:: 200080045

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 2000800437.

Chromatin environment, transcriptional regulation and splicing distinguish lncRNAs and mRNAs [NucFrac]

Organism:: Homo sapiens

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

Platform:: GPL11154
4 Samples

Download data: TXT

Series

Accession:: GSE80043

ID:: 200080043

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2002187268.

Modeling the nascent RNA transcriptome with chrTT-seq to extract chromatin dissociation dynamics on newly transcribed RNA.

(Submitter supplied) To capture chromatin dissociation dynamics of nascent RNA transcripts we labeled MCF-7 cells with 4-thio-uridine (4-SU) for 8 minutes, then chased with an excess of uridine for 5, 10, 15 and 20 min. At each pulse-chase time point we performed TT-seq from the chromatin-associated and nucleoplasmic fraction. The ratios of spike-in normalized chromatin-associated to chromatin-released nascent RNA read coverage over genomic features (transcripts' last exons) were fitted on an exponential decay function to extract an estimated chromatin association half-live time for each transcript.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL16791
10 Samples

Download data: BW

Series

Accession:: GSE218726

ID:: 200218726

Select item 2000698429.

Illumina Total RNA-seq in HeLa

(Submitter supplied) Purpose: Examine the effect of the long non-coding RNA PARROT on the transcriptome in HeLa cells.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
8 Samples

Download data: BW, RPKM

Series

Accession:: GSE69842

ID:: 200069842

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 20005853410.

PARP1- and CTCF-mediated interactions between active and repressed chromatin at the lamina promote oscillating transcription

(Submitter supplied) Transcriptionally active and inactive chromatin domains tend to segregate into separate sub-nuclear compartments to maintain stable expression patterns. However, we have uncovered here an inter-chromosomal network connecting active loci enriched in circadian genes to repressed lamina-associated domains (LADs). The interactome is regulated by PARP1 and its co-factor, CTCF, which not only mediate chromatin fiber interactions, but also promote the recruitment of circadian genes to the lamina. more...

Organism:: Homo sapiens

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

Platform:: GPL16791
2 Samples

Download data: BED

Series

Accession:: GSE58534

ID:: 200058534

PubMed Similar studies SRA Run Selector

Select item 20002688011.

PARP1- and CTCF-mediated interactions between active and repressed chromatin at the lamina promote oscillating transcription

Organism:: Homo sapiens

Type:: Other; Expression profiling by high throughput sequencing

Platforms:: GPL15520 GPL16791 GPL9115
23 Samples

Download data: TXT

Series

Accession:: GSE26880

ID:: 200026880

Select item 20001935512.

Silencing of mrhl non coding RNA in mouse spermatoginial cells GC1-Spg

(Submitter supplied) Mrhl is a non coding RNA identified from mouse chromosome 8. It is a 2.4kb poly adenylated, nuclear restricted RNA expressed in multiple tissues. The 2.4 kb RNA also undergoes a nuclear processing event mediated through Drosha that generates an 80nt intermediate RNA. This study was aimed at understanding the functiion of mrhl by silencing the mrhl RNA in the mouse spermatogonial cells using a pool of siRNAs targeted against the mrhl and analyse the global gene expression change using Affymetrix mouse expression array. more...

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL1261
6 Samples

Download data: CEL

Series

Accession:: GSE19355

ID:: 200019355

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20006614013.

RNA-Seq analysis of mouse liver lincRNAs

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

Organism:: Mus musculus

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

Platforms:: GPL17021 GPL13112
36 Samples

Download data: BW

Series

Accession:: GSE66140

ID:: 200066140

PubMed Full text in PMC Similar studies

Select item 20006600914.

Gene expression profile of hepatic lincRNAs in male mouse liver using nuclear RNA-Seq

(Submitter supplied) Gene expression in adult male mouse liver was assayed by nuclear RNA-seq, as part of a study of hepatic lincRNAs.

Organism:: Mus musculus

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

Platform:: GPL17021
3 Samples

Download data: XLSX

Series

Accession:: GSE66009

ID:: 200066009

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20006600815.

Response of liver-expressed genes (including lincRNAs) to continuous growth hormone (GH) infusion

(Submitter supplied) Gene expression in livers of adult male mice subjected to continuous GH infusion using Alzet osmotic minipumps for 1, 4 or 7 days was assayed by RNA-seq, as part of a study of growth hormone regulation of hepatic lincRNAs (PMID:26459762) and protein-coding genes (PMID:28694329).

Organism:: Mus musculus

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

Platform:: GPL13112
12 Samples

Download data: BW, XLSX

Series

Accession:: GSE66008

ID:: 200066008

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20006600716.

Gene expression profile of hepatic lincRNAs in female mouse liver using nuclear RNA-Seq

(Submitter supplied) Gene expression in adult female mouse liver was assayed by nuclear RNA-seq, as part of a study of hepatic lincRNAs.

Organism:: Mus musculus

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

Platform:: GPL13112
3 Samples

Download data: BW, XLSX

Series

Accession:: GSE66007

ID:: 200066007

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20006600317.

Gene expression profile of intact and hypophysectomized adult male and female mouse liver

(Submitter supplied) Gene expression in intact and hypophysectomized adult mouse liver was assayed by RNA-seq analysis of total liver RNA, as part of a study of growth hormone regulation of hepatic lincRNAs.

Organism:: Mus musculus

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

Platform:: GPL13112
8 Samples

Download data: BW, XLSX

Series

Accession:: GSE66003

ID:: 200066003

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20006600118.

Gene expression profile of adult male mouse liver using total liver RNA-seq and nuclear liver RNA-Seq

(Submitter supplied) Gene expression in male mouse liver was assayed by RNA-seq, as part of a study to study cellular compartmentalization of hepatic lincRNAs.

Organism:: Mus musculus

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

Platform:: GPL13112
4 Samples

Download data: BW, XLSX

Series

Accession:: GSE66001

ID:: 200066001

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20006600019.

Identification of sex-specific hepatic lincRNAs using nuclear RNA-Seq

(Submitter supplied) Gene expression in adult male and female mouse liver was analyzed based on nuclear RNA-seq, as part of a study on hepatic lincRNAs.