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Sample GSM5360276 Query DataSets for GSM5360276
Status Public on Oct 31, 2021
Title Test_3217_MOET
Sample type SRA
 
Source name Testicle
Organism Bos taurus
Characteristics embryo origin: MOET
age (days): 102
weight at birth (kg): 35
weight at sample collection (kg): 131
Sex: Male
tissue: Testicle
breed: Holstein
individual: 3217
Treatment protocol Holstein embryos were produced in vitro or in vivo (by ovarian superstimulation followed by AI) and transferred to synchronized recipients. Pregnancies were monitored until delivery when the birthweights of the calves were recorded. Calves were maintained in similar condition during the postnatal period until euthanasia at around 100 days of age.
Extracted molecule total RNA
Extraction protocol Tissues samples were shipped in dry ice to the BGI TECH SOLUTIONS Company (Hong Kong), which performed the RNA extraction, quality control, library preparation and sequencing. All samples met the requirements for library preparation (adequate concentration and quantity, purity as OD260/280 = 1.8~2.0 and RIN > 7).
RNA sequencing (RNAseq) was run in the RNA samples through non-stranded & polyA-selected mRNA library preparation and PE100 sequencing with 5Gb clean data per sample on DNBSEQ. After library preparation and sequencing, raw data with adapter sequences or low-quality sequences were filtered to remove contamination and obtain valid data. This step was completed by the SOAPnuke software developed by BGI Company.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-G400
 
Data processing The RNAseq read pairs were mapped to the bovine reference genome (bosTau9) with STAR aligner (v. 2.7), generating the genome index with the gene Bos taurus release 102 annotation.
Read counts were estimated at gene level using HTSeq-count.
Genome_build: bosTau9
Supplementary_files_format_and_content: *.txt: Tab-delimited text files containing raw read counts for each sample.
 
Submission date Jun 05, 2021
Last update date Oct 31, 2021
Contact name Maria Belen Rabaglino
E-mail(s) m.b.rabaglino@uu.nl
Organization name Utrecht University
Department Population Health Science
Street address Yalelaan 7
City Utrecht
ZIP/Postal code 3584 CL
Country Netherlands
 
Platform ID GPL28857
Series (1)
GSE176219 Transcriptomics of the HPG axis from in vitro or in vivo-produced dairy male calves
Relations
BioSample SAMN19580561
SRA SRX11075246

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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