|
| Status |
Public on Dec 13, 2021 |
| Title |
166-2019_S39 |
| Sample type |
SRA |
| |
|
| Source name |
Whole blood
|
| Organism |
Bos taurus |
| Characteristics |
arrival weight (lbs): 511
times treated: 1
disease severity cohort: Treated Once
tissue: Whole blood
|
| Treatment protocol |
All blood samples were collected in Tempus blood tubes (Applied Biosystem). Samples were stored per product recommendation.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA purification and extraction was performed with the Tempus Spin RNA Isolation kit (Applied Biosystems), per product instructions. RNA concentration and quality was measured with an Agilent 2100 (Agilent).
Library construction was performed with the TruSeq RNA Sample Library Kit (Illumina). 150bp paired-end sequencing was performed with an Illumina Novaseq 6000 (v1.7; S4 reagent kit v1.5) in one lane (~50M reads/sample).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Sex: S
|
| Data processing |
Illumina RTA v3 software was used for basecalling.
Read quality was assessed in FastQC v0.11.9
Read trimming was performed with Trimmomatic v0.39 with parameters for a 4-base pair sliding window and removing read segments below a minimum base quality score of 20 and a read length of less than 36 bases
Read mapping and indexing was performed with HISAT2 v2.1.1, using the bovine whole genome assembly ARS-UCD1.2; parameters -p 8 --dta -x GCF_002263795.1_ARS-UCD1.2_genomic
Read assembly and quantification was performed with StringTie v2.1.2 with parameters -p 8 -G ref_ARS-UCD1.2, followed by ./stringtie --merge -p 8 -G ref_ARS-UCD1.2, and /stringtie -e -p 8 -G stringtie_merge.gtf -o. A read count matrix was generated with prepDE.py with parameters python2.7 ./prepDE.py -l 150 -i mergelist.txt. Differential expression analysis was performed with edgeR v3.30.3.
Genome_build: GCF_002263795.1
Supplementary_files_format_and_content: tab-delimited text file of gene counts for each sample
|
| |
|
| Submission date |
Nov 12, 2020 |
| Last update date |
Dec 14, 2021 |
| Contact name |
Matthew Adam Scott |
| E-mail(s) |
matthewscott@tamu.edu
|
| Organization name |
Texas A&M University
|
| Department |
Large Animal Clinical Sciences
|
| Street address |
3201 Russell Long Blvd
|
| City |
Canyon |
| State/province |
TX |
| ZIP/Postal code |
79015 |
| Country |
USA |
| |
|
| Platform ID |
GPL26012 |
| Series (1) |
| GSE161396 |
Multipopulational transcriptome analysis of beef cattle at arrival to identify and further validate candidate biomarkers for predicting clinical bovine respiratory disease |
|
| Relations |
| BioSample |
SAMN16786609 |
| SRA |
SRX9500763 |
