|
| Status |
Public on Jun 30, 2022 |
| Title |
Liver_3217_MOET |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Bos taurus |
| Characteristics |
embryo origin: MOET
age (days): 102
weight at birth (kg): 35
weight at sample collection (kg): 131
Sex: Male
tissue: Liver
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: GeneCounts_LiverMuscle.txt: Tab-delimited text file containing raw read counts for each sample.
|
| |
|
| Submission date |
Feb 17, 2022 |
| Last update date |
Jun 30, 2022 |
| 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) |
| GSE196974 |
Transcriptomics of the liver and the muscle from in vitro or in vivo-produced dairy male calves |
|
| Relations |
| BioSample |
SAMN26027320 |
| SRA |
SRX14213595 |
