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Homo sapiens

ABSTRACT: Exploring the gene expression profile upon FXR1 knockdown in H358 cells using RNA-seq

PROVIDER: PRJNA395359 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5859120_1.fastq.gz	Fastqsanger.gz
	SRR5859120_2.fastq.gz	Fastqsanger.gz
	SRR5859130_1.fastq.gz	Fastqsanger.gz
	SRR5859130_2.fastq.gz	Fastqsanger.gz
	SRR5859121_1.fastq.gz	Fastqsanger.gz

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Exploring the gene expression profile upon FXR1 knockdown in H358 cells using RNA-seq

Project description:We performed the RNA-seq in control samples and FXR1 knockdown samples, and compared the gene expression profiles to explore the effect of FXR1 knockdown on gene expression. The study was performed in H358 cells. Doxycycline inducible shRNA3 (sh3) was used to knockdown FXR1. Control shRNA (ctrl) samples were used to get rid of the effect of Doxycycline treatment. Both the Doxycycline treament for 3 days (D3) and 5 days (D5) samples were collected. Each sample has three repeats (rep 1, rep 2, and rep 3). The mRNA profiles were generated by deep sequencing using Illumina.Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using STAR v2.5.3 with parameters --bamRemoveDuplicatesType UniqueIdentical --outSAMmultNmax 1. Raw reads and Reads Per Kilobase per Megabase of library size (RPKM) were calculated using HOMER (PMID: 20513432). Differential gene expression was analyzed using R package DESeq2 using the raw reads.

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Exploring the occupancy and interaction with FXR2, STAT1/3 and H3K4me3 at genomic level of FXR1 in H358 and AGS cell line by ChIP-seq

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