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Sample GSM6945905

Query DataSets for GSM6945905

Status

Public on Jun 03, 2023

Title

MCT 3

Sample type

SRA

Source name

Liver

Organism

Sus scrofa domesticus

Characteristics

dose: Isovolumetric Vehicle Control (3ml/kg)
breed: Yorkshire
tissue: Liver
treatment: MCT

Extracted molecule

total RNA

Extraction protocol

Liver sections were flash frozen in liquid nitrogen and stored a -80C. RNA was harvested using the Trizol method.
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene, Inc.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

Exp_3

Data processing

Data processing was performed by Novogene Inc: "Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed."
Assembly: GCF_000003025.6
Supplementary files format and content: Processed data are provided as a tab-delimited text file including read counts for all genes across all samples, including FPKM values

Submission date

Jan 20, 2023

Last update date

Jun 03, 2023

Contact name

Scott C Fligor

Organization name

Boston Children's Hospital

Department

Surgery

Street address

300 Longwood Ave