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| Status |
Public on May 25, 2016 |
| Title |
AA_2 |
| Sample type |
SRA |
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| Source name |
AA, whole blood
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| Organism |
Equus caballus |
| Characteristics |
tissue: whole blood
cell type: circulating leukocytes
snp allelic state: AA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Life Technologies MagMax RNA isolation kit
Illumina true seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
140
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| Data processing |
Reads were mapped and aligned with Tophat 2.0.14
HT-Seq was used to generate read count tables for each sample using the equCab2 Ensembl annotation, HT-Seq intersection non-empty, and merged in counts.txt
counts.txt loaded in to edgeR to identify differentially expressed genes (AAvsABBB_TopTags.txt)
cufflinks was used to generate transcripts.gtf
cuffdiff generated AA_ABBB_gene_exp.diff to identify differentially expressed genes
Genome_build: EquCab2.0
Supplementary_files_format_and_content: abundance measurements and differentially expressed genes
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| Submission date |
May 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Cole M McQueeen |
| E-mail(s) |
cmcqueen@cvm.tamu.edu
|
| Organization name |
Texas A&M University
|
| Street address |
4467 VMRB
|
| City |
College Station |
| ZIP/Postal code |
77843 |
| Country |
USA |
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| Platform ID |
GPL21941 |
| Series (1) |
| GSE81858 |
RNA-Seq identifies differential gene expression associated with risk-genotype for Rhodococcus equi pneumonia in horses |
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| Relations |
| BioSample |
SAMN05176206 |
| SRA |
SRX1799613 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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