GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM5032518

Query DataSets for GSM5032518

Status

Public on Apr 01, 2021

Title

CA29

Sample type

SRA

Source name

caruncle

Organism

Bos taurus

Characteristics

tissue: placental caruncle
developmental stage: 83 days of preganancy
farm: 1
treatment: VTM_LG

Treatment protocol

The factors examined included vitamin and mineral supplementation (VTM or NoVTM) and rate of gain (low gain – LG or moderate gain – MG). The treatments were arranged as follows: (1) no vitamin and mineral supplementation and low gain (NoVTM_LG, n = 9); (2) vitamin and mineral supplementation and low gain (VTM_LG, n = 9); (3) no vitamin and mineral supplementation and moderate gain (NoVTM_MG, n = 9), and (4) vitamin and mineral supplementation and moderate gain (VTM_MG, n = 8).

Extracted molecule

total RNA

Extraction protocol

Total RNA of eight female samples per treatment was isolated from the CAR and COT tissues using the RNeasyâ kit (Qiagenâ, Germantown, MA) followed by on-column DNase treatment, according to the manufacturer's protocol.
Strand-specific RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA). Library preparation and paired-end sequencing with 150-bp reads at a depth of 20 M reads/sample were carried out at Novogene Co. (Nanjing, China).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Illumina Casava software
Sequencing adaptors, low-complexity reads, and reads containing low quality bases were removed in an initial data-filtering step. Reads with a PhredScore lower than 30 were filtered out. Quality control (QC) and read statistics were estimated with FastQC v0.11.8 and MultiQC v1.9 software. After QC, 29 and 31 samples (seven or eight samples per group) remained for further analyses from CAR and COT, respectively. Reads were mapped to the Bos taurus reference genome (ARS-UCD 1.2) [31] using the STAR aligner v. 2.7.3a. Raw counts per gene were obtained using the –quantMode GeneCounts flag from STAR based on the gene annotation file (release 100, Ensembl). MultiQC, NOISeq, and edgeR software were used to perform the post-mapping quality control. Genes with expression values lower than 1 count per million in 50% of the samples were filtered out. After filtering, the genes of CAR and COT tissues were analyzed using the DESeq2 v.1.22.1 software to identify DEGs.
Genome_build: Bos taurus ARS-UCD 1.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every tissue, gene and every sample

Submission date

Jan 22, 2021

Last update date

Apr 01, 2021

Contact name

Wellison J. S. Diniz

Organization name

Auburn University

Department

Animal Sciences

Lab

Livestock Genomics & Bioinformatics