Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparison of genomic binding profile for several transcription factors and 3' processing factors in control and CFIm25 KD hESCs (H9 cell line)

ABSTRACT: To understand how CFIm25 depletion affects gene expression at the transcription level, we carried out ChIP-seq analysis for several transcription factors and 3' processing factors in control and CFIm25 KD cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE178075 | GEO | 2022/04/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Comparison of genomic binding profile for CFIm25 in control and CFIm25 KD hESCs (H9 cell line)

Project description:To understand how CFIm25 associates with genomic DNA during co-transcriptional mRNA processing,we carried out ChIP-seq analysis for CFIm25 in control and CFIm25 KD cells (CFIm25 KD cells as normalization background)

2022-04-21 | GSE178076 | GEO

poly(A+)-seq profiling of gene expression in control H9 and (CFIm25 KD+ 3Flag-CFIm25 overexpression) H9 cell lines

Project description:We carried out CFIm25 KD experiments in H9 cell line (hESCs). After poly(A+)-seq, we found the expression of hundreds of genes were changed. To investigate if the effect is a direct or indirect effect of CFIm25 KD, we next carried out 3Flag-CFIm25 overexpression in CFIm25 KD cells for gene-rescue experiments. After we obtained this cell line, here we performed poly(A+)-seq in control H9 and (CFIm25 KD+ 3Flag-CFIm25 overexpression)H9 cell lines. The goal of this experiment is to investigate if CFIm25 overexpression could rescue the gene expression phenotype caused by CFIm25 KD.

2022-04-21 | GSE176328 | GEO

Comparison of genomic binding profile for RNA polyII in control and CFIm25 KD hESCs (H9 cell line)

Project description:To understand how CFIm25 depletion affects gene expression at the transcription level, we carried out ChIP-seq analysis for RNAPII in control and CFIm25 KD cells.

2022-04-21 | GSE176543 | GEO

Comparison of genomic binding profile for several transcription factors and 3' processing factors in control and CFIm25 KD hESCs (H9 cell line)

Project description:Comparison of genomic binding profile for several transcription factors and 3' processing factors in control and CFIm25 KD hESCs (H9 cell line)

| PRJNA737293 | ENA

Global poly(A+) RNA-seq profiling in control and CFIm25 KD human embryonic stem cells (H9 cell line)

Project description:To understand how CFIm25, an mRNA 3' processing regulator, affects the global poly(A+) RNAs profiling in hESCs (H9 cell line). We carried out poly(A+)-seq in control (2 samples) and CFIm25 KD (3 samples) hESCs.Using a cutoff value (P<0.05, fold change>1), in total, 577 differentially expressed genes (268 down-regulated genes and 309 up-regulated genes) were found upon CFIm25 KD, and the number of down-regulated genes and up-regulated genes were 84 and 128 respectively if using the cutoff value (P<0.05, fold change>2).

2022-04-21 | GSE176327 | GEO

Comparison of genomic binding profile for CFIm25 in control and CFIm25 KD hESCs (H9 cell line)

Project description:Comparison of genomic binding profile for CFIm25 in control and CFIm25 KD hESCs (H9 cell line)

| PRJNA737294 | ENA

Global PAS-seq (polyA-site-sequencing) profiling in control and CFIm25 KD human embryonic stem cells (H9 cell line)

Project description:To understand how CFIm25, an mRNA 3' processing regulator, affects global mRNA alternative polyadenylation (APA) profiling in H9 cells. We performed PAS-seq (polyadenylation site sequencing) in control (2 samples) and CFIm25 KD cells (3 samples). PAS-seq library was prepared using a lexogen kit (3'-seq, Catolog. 016.024). Sequencing was performed using Novaseq PE150.

2022-04-21 | GSE176343 | GEO

poly(A+)-seq profiling of gene expression in control H9 and (CFIm25 KD+ 3Flag-CFIm25 overexpression) H9 cell lines

Project description:poly(A+)-seq profiling of gene expression in control H9 and (CFIm25 KD+ 3Flag-CFIm25 overexpression) H9 cell lines

| PRJNA735770 | ENA

Comparison of genomic binding profile for RNA polyII in control and CFIm25 KD hESCs (H9 cell line)

Project description:Comparison of genomic binding profile for RNA polyII in control and CFIm25 KD hESCs (H9 cell line)

| PRJNA736678 | ENA

CFIm25 links alternative polyadenylation to glioblastoma tumour suppression

Project description:Purpose: To identify all of the APA targets of CFIm25 on a global scale and develop an algorithm that can idenitify APA events from standard RNA-seq data Methods: RNA from HeLa cells treated with control siRNA and CFIm25 siRNA were subject to RNA-Seq. Using a custom-designed algorithm to mine RNA-seq data for novel APA events regulated by CFIm25. Results: We identified over 1,400 genes with shortened 3’UTRs after CFIm25 knockdown. Importantly, we show that as a consequence of APA, many of these mRNAs have greatly enhanced protein expression due to the loss of destabilizing features within the 3’UTR. Conclusions: Our study underscored the critical function of the CFIm complex members in governing APA and establish a previously unknown link between APA and metabolic pathways important for tumor progression. Hela cell line mRNA profiles of control treated and CFIm25 Knockdown were generated by RNA-Seq using Illumina GAIIx.

2014-05-15 | E-GEOD-42420 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data