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Sample GSM7963998

Query DataSets for GSM7963998

Status

Public on Sep 02, 2024

Title

adipose, control rep 4

Sample type

SRA

Source name

adipose

Organism

Sus scrofa

Characteristics

tissue: adipose
genotype: Iberian pig
treatment: C

Treatment protocol

50-100 mg samples of each tissue were ground in liquid nitrogen with mortar and pestle.

Growth protocol

Subcutaneous adipose tissue was collected within 15 min postmortem, snap-frozen in liquid nitrogen, and then stored at -80° C until processing.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted from 50-100mg samples of adipose tissue using the RiboPure TM of High Quality total RNA kit (Ambion, Austin, TX, USA) following the manufacturer’s recommendations. RNA was quantified using a NanoDrop-100 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The quality of the RNA was evaluated using the RNA Integrity Number (RIN) value from the Agilent 2100 Bioanalyzer device (Agilent technologies, Santa Clara, CA, USA).
Sequencing libraries were made using the mRNA-Seq sample preparation kit (Illumina Inc., Cat. # RS-100-0801) according to manufacturer’s protocol. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired end mode with the read length 2x76bp on a on a NovaSeq 6000 (Illumina, Inc). Images from the instrument were processed using the manufacturer’s software to generate FASTQ sequence files.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to assess the quality of raw sequencing data.
TrimGalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to quality trim data with default settings and to remove the sequencing adaptors and poly A and T tails (stringency of 6 bp, -s 6) keeping only paired-end reads where both pairs were longer than 40 bp.
Filtered reads were mapped against the pig reference genome (Sscrofa11.1) using HISAT2 applying default settings except that reads were first aligned to the ENSEMBL (11.1.90) transcriptome annotation (-G option), and the distance between both pairs was set to 100 bp (inner-mean distance) and the standard deviation to 150 bp.
HTseq-counts was used to calculate transcript abundances. Differential expression was analysed with Deseq2
Assembly: Sscrofa 11.1
Supplementary files format and content: Processed data file includes read counts for all genes in all 24 samples

Submission date

Dec 08, 2023

Last update date

Sep 02, 2024

Contact name

Cristina Ovilo

E-mail(s)

ovilo@inia.csic.es

Organization name

INIA-CSIC

Street address

Ctra Coruña km 7.5