|
| Status |
Public on Jan 14, 2020 |
| Title |
BRD 6 [S_85] |
| Sample type |
SRA |
| |
|
| Source name |
BRD_whole blood
|
| Organism |
Bos taurus |
| Characteristics |
arrival weight (lbs.): 400
disease status: bovine respiratory disease (BRD)
tissue: whole blood
|
| Treatment protocol |
All blood samples were collected in Tempus blood tubes (Applied Biosystem). Samples were stored per product recommendation.
|
| Extracted molecule |
total 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).
Paired end libraries were prepared using the TruSeq stranded mRNA kit. All samples were generated in 2 x 150 base pair lengths, in 2 lanes, at 80 million reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
85_S12
|
| Data processing |
Illumina RTA v2 software was used for base calling.
Read quality was assessed in FastQC v0.11.8
Read trimming was performed with Trimmomatic v0.38 with parameters ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Read mapping and indexing was performed with HISAT2 v2.1.0, 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 v1.3.4 with parameters -p 8 -G ref_ARS-UCD1.2_top_level, followed by ./stringtie --merge -p 8 -G ref_ARS-UCD1.2_top_level, 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 -i mergelist.txt. Differential expression analysis was performed with edgeR v3.24.3 and DESeq2 v1.22.2.
Genome_build: GCF_002263795.1
Supplementary_files_format_and_content: tab-delimited text file of gene counts for each sample
|
| |
|
| Submission date |
Aug 22, 2019 |
| Last update date |
Jan 15, 2020 |
| Contact name |
Matthew Adam Scott |
| E-mail(s) |
[email protected]
|
| 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 |
GPL21659 |
| Series (1) |
| GSE136176 |
Whole blood transcriptomic analysis of beef cattle at arrival identifies potential predictive molecules and mechanisms that indicate animals that naturally resist bovine respiratory disease |
|
| Relations |
| BioSample |
SAMN12619313 |
| SRA |
SRX6763585 |
