|
| Status |
Public on Feb 28, 2020 |
| Title |
NB_116 (pwbc) |
| Sample type |
SRA |
| |
|
| Source name |
peripheral white blood cells
|
| Organism |
Bos taurus |
| Characteristics |
heifer id: 116
tissue: peripheral white blood cells
classification: NB-pregnant
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from PWBCs of 18 heifers (AI-pregnant (n=6), NB-pregnant (n=6), and not pregnant (n=6)) using TRIzol reagent following the manufacturer’s protocol. Total RNA (circulating extracellular RNA) was isolated from 1ml of plasma by adding 9 ml of TRIzol reagent and following manufacturer’s protocols through organic phase separation. The aqueous phase containing the RNA was then collected and purified with the RNA Clean & Concentrator-5 kit, according to manufacturer’s instructions.
Aproximatly 500 mg of total RNA was used as input for the TruSeq Stranded mRNA Library Prep kit. Total RNA obtained from plasma was desiccated to a volume of 2.5ul for library preparation with the TruSeq Small RNA Library Prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were aligned to the bovine genome (ARS-UCD1.2 obtained from Ensembl) using HISAT2 (version 2.1.0)
The sequences were then marked for duplicates, and non-duplicated pairs of reads (mRNA) or single reads (miRNA) were used for transcript quantification at the gene level. The fragments were counted against the Ensembl gene annotation (version 1.87) using featureCounts (version 1.6.0)
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample
|
| |
|
| Submission date |
Feb 27, 2020 |
| Last update date |
Feb 28, 2020 |
| Contact name |
Fernando H Biase |
| E-mail(s) |
fbiase@vt.edu
|
| Phone |
540-231-9520
|
| Organization name |
Virginia Tech
|
| Department |
School of Animal Sciences
|
| Lab |
Biase lab
|
| Street address |
175 West Campus Drive
|
| City |
Blacksburg |
| State/province |
VA |
| ZIP/Postal code |
24061 |
| Country |
USA |
| |
|
| Platform ID |
GPL26012 |
| Series (1) |
| GSE146041 |
Rewiring of gene expression in PWBC at artificial insemination is predictive of pregnancy outcome in cattle (Bos taurus) |
|
| Relations |
| BioSample |
SAMN14238374 |
| SRA |
SRX7814237 |
