Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 36
Release date: Jan 11 2018
Last update date: Oct 22 2018
Access: Public
Taxon: Rattus norvegicus
Computational protocol: ea-utils, Subread, DESeq2
Dataset link Selection of well-tolerated GalNAc-conjugated siRNAs by screening for RNAi-mediated off-target effects in rodent toxicity studies

Experimental Protocol


RNASeq analysis of hepatotoxicity Rat livers were collected 24 h post-50 mg/kg single dose of GalNAc-siRNAs and snap-frozen. Rat hepatocytes (BioreclamationIVT) were transfected with 10 nM GalNAc-siRNAs using Lipofectamine RNAiMAX (Thermo Fisher Scientific) according to manufacturer’s instructions, and harvested 24 h post-transfection. Rat hepatocytes were not tested for mycoplasma contamination. RNA extracted with the miRNeasy kit (Qiagen) was used for cDNA library preparation with the TruSeq Stranded Total RNA Library Prep Kit (Illumina) and sequenced on the HiSeq or NextSeq500 sequencers (Illumina), all according to manufacturers’ instructions. Raw RNAseq reads were filtered with minimal mean quality scores of 25 and minimal remaining length of 36, using fastq-mcf. Filtered reads were aligned to the Rattus norvegicus genome (Rnor_6.0) using STAR (ultrafast universal RNA-seq aligner) with default parameters. Uniquely aligned reads were counted by featureCounts. Differential gene expression analysis was performed by the R package DESeq2.The open source DESeq2 R package was used for the RNAseq data analysis.

Repositories


GEO

GSE108823

ENA

SRP128126

BioProject

PRJNA428745

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Contact


Joseph Barry

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