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

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

PROVIDER: PRJNA735770 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14751361_1.fastq.gz	Fastqsanger.gz
	SRR14751361_2.fastq.gz	Fastqsanger.gz
	SRR14751362_1.fastq.gz	Fastqsanger.gz
	SRR14751362_2.fastq.gz	Fastqsanger.gz
	SRR14751363_1.fastq.gz	Fastqsanger.gz

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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.

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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).

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

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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.

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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)

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

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