|
| Status |
Public on Aug 01, 2018 |
| Title |
Day 42 Neinke 2014 foal |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood mononuclear cells
|
| Organism |
Equus caballus |
| Characteristics |
age: day 42
Sex: male
breed: Warmblood
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral blood mononuclear cells (PBMC) were isolated from blood samples and stored at -80C. RNA was isolated with the RNeasy kit including on-column DNase I digestion, as directed (Qiagen, Valencia CA).
RNA libraries were prepared as directed by the Illumina TruSeq Stranded mRNA Library Prep Kit. Samples were barcoded for multiplexing with the following adapters: day 1 Inga foal index 2; day 1 Konstance foal index 4; day 1 Wild Rose foal index 5; day 1 Neinke 2014 foal index 6; day 42 Inga foal index 7; day 42 Konstance foal index 12; day 42 Wild Rose foal index 13; day 42 Neinke 2014 foal index 14; Inga mare index 15; Holly mare index 16; Wild Rose mare index 18; Neinke mare index 19
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
FASTQC software used for quality check
Sequenced reads were trimmed for adaptor sequence, filter low-quality sequence
Trimmed reads were aligned to the equine genome sequence (NCBI reference assembly EquCab2.0) with TopHat version 2.1.1
Cuffdiff version 2.2.1 was used to get raw read count at gene level
edgeR was for normalization and statistical analysis for identifying differentially expressed genes
Genome_build: NCBI reference assembly EquCab2.0
Supplementary_files_format_and_content: abundance measurements
|
| |
|
| Submission date |
Jul 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Wojciech Pawlowski |
| E-mail(s) |
mw729@cornell.edu
|
| Organization name |
Cornell University
|
| Department |
Plant Breeding and Genetics
|
| Street address |
Bradfield Hall, Room 403
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL21401 |
| Series (1) |
| GSE101117 |
Dynamic immune gene expression in young foals |
|
| Relations |
| BioSample |
SAMN07340765 |
| SRA |
SRX2994648 |
