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Sample GSM1936069

Query DataSets for GSM1936069

Status

Public on Jun 07, 2016

Title

A03927_D50

Sample type

SRA

Source name

Milk somatic cells

Organism

Ovis aries

Characteristics

day of lactation: Day 50
breed: Assaf
cell type: MSC

Extracted molecule

total RNA

Extraction protocol

MSCs were pelleted using PBS and EDTA. RNA was harvested using Trizol (Invitrogen, Carlsbad, CA, USA). Paired-end libraries were obtained using the True-Seq RNA-Seq sample preparation Kit v2 (Illumina, San Diego, CA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Illumina Casava1.7 software used for basecalling.
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to assess the quality of raw sequencing data. Reads were mapped against the ovine genome assembly v.3.1. (Oar_v3.1) using STAR aligner (v.2.3.1y)
The Cufflinks (Cufflinks v.2.1.1) option “–g” followed by the available gtf file from the Oar_v3.1 reference sequence was used to guide the assembly but not excluding new genes. Cuffmerge was used to filter genes with low or no expression from our reference gtf file.
SigCufflinks (available at http://www.sigenae.org) was used to obtain raw counts per gene
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: csv file with raw counts per gene and sample

Submission date

Nov 09, 2015

Last update date

May 15, 2019

Contact name

Juan-Jose Arranz

E-mail(s)

[email protected]

Phone

+34 987291470

Organization name

Universidad de Leon