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Genome wide RNA sequencing to profile response to IL-1 in control and IFT88 depleted cells

ABSTRACT: Genome wide RNA sequencing to profile response to IL-1 in control and IFT88 depleted cells

PROVIDER: PRJNA528023 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8752290_1.fastq.gz	Fastqsanger.gz
	SRR8752290_2.fastq.gz	Fastqsanger.gz
	SRR8752300_1.fastq.gz	Fastqsanger.gz
	SRR8752300_2.fastq.gz	Fastqsanger.gz
	SRR8752310_1.fastq.gz	Fastqsanger.gz

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Genome wide RNA sequencing to profile response to IL-1 in control and IFT88 depleted cells

Project description:Purpose: RNA sequencing across whole genome downstream to IL-1 to investigate scope and nature of effect of IFT88 depletion Method: Control pool treated and IFT88 siRNA pool targeted Fibroblast-like chondrocytes were treated with or without IL-1B 10ng/ml and RNA collected in triplicate at 0, 1, 2, 4, 8 and 24h. PolyA-selected sequencing libraries were prepared using the TruSeq protocol (Illumina). Libraries were subject to 75bp paired-end sequencing (Illumina HiSeq 4000) to an average depth of 28.5 million read pairs per sample and aligned to mouse genome with Hisat2. Results: Using time-course analysis (ImpulseDE2) the IL-1 response timecourse was determined (control-only) and intersected against the comparative case vs control analysis. Per-point differential expression analysis IFT88 vs control was performed using DESeq2. Conclusion: Demonstration of the effect of IFT88 depletion on IL-1 response signature over 24h.

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