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Sample GSM4794656

Query DataSets for GSM4794656

Status

Public on Oct 06, 2021

Title

NASH_20

Sample type

SRA

Source name

Liver

Organism

Cavia porcellus

Characteristics

strain: Dunkin Hartley
diet: High fat diet
time on diet: 25 weeks
disease state: NASH
tissue: Liver

Treatment protocol

Animals were given either a chow, or high fat diet for 25 weeks.

Extracted molecule

total RNA

Extraction protocol

Liver sections from the left lateral lobe were snap frozen in liquid nitrogen. 12-24 mg of liver from each sample was sent to Qiagen for purification.
500 ng of total RNA was enriched for mRNA by using oligodT bead system. Library preparation was performed by Qiagen using the TruSeq mRNA sample preparation kit (Illumina Inc.), and standard Illumina protocols.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Description

N20
Total mRNA
raw_counts_GP.txt
GP_rlogs.txt

Data processing

Base calling was performed on NextSeq500 (Illumina) using RTA 2.0, and the resulting BCL files were converted to fastq files using the bcl2fastq software (Illumina).
Fastq files were trimmed for adaptor sequences and any reads below 50 nt. were discarded using the Trimmomatic 0.38.0 software with the input HEADCROP: 9, MINLEN: 50
The trimmed reads were mapped using the HISAT2 2.1.0 mapper. The Cavia Porcellus genome and annotation (CavPor.3.0.98) was acquired from Ensembl, and used as reference genome.
Initial transcript assembly was performed by StringTie 1.3.6 using the guinea pig annotation file (CavPor.3.0.98) as a guide. StringTie merge 1.3.6 was run on Stringtie output from all samples with the guinea pig annotation file as a guide, and default parameters. For quantification StringTie was run on the StringTie merge file separately for each sample by using the guinea pig annotation file as a guide, setting the -e parameter was set to "yes" and the output type to deseq2.
Raw counts for each StringTie file was assembled into a collected file and to obtain translatability and more annotation, BioMart was used to find human orthologs for each transcript. To diminish background noise genes with raw counts below 200 across all samples were discarded. Finally Deseq2 was used for differential expression.
Genome_build: CavPor3 (Cavpor3.0)
Supplementary_files_format_and_content: raw_counts_GP.txt: Matrix file with raw counts for each Cavia Porcellus gene ID and each sample.
Supplementary_files_format_and_content: GP_rlogs.txt: Normalized and transformed values (normalized according to DESeqs' size factor, and rlog transformed) for each sample, and each gene (gene names are obtained by finding human orthologs).

Submission date

Sep 17, 2020

Last update date

Oct 06, 2021

Contact name

Josephine Skat-Rørdam

E-mail(s)

[email protected]

Organization name

Københavns Universitet

Department

Department of Veterinary and Animal Sciences