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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

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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)

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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)

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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

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

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)

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

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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)

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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

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