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| Status |
Public on Feb 18, 2019 |
| Title |
Control 2 |
| Sample type |
SRA |
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| Source name |
Blood
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| Organism |
Bos taurus |
| Characteristics |
copper levels in blood (avg for 3 individuals): 24.58
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested using a Qiagen RNEasy kit with 1 ug of total RNA used for the construction of the sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols for stranded libraries
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
blood pooled from three individuals
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| Data processing |
alignment with STAR v 2.5.1b, controlling for unannotated, non-canonical and rare junctions
read count generation during STAR alignment using –quantmode GeneCounts option that works like HTSeq-Count in default mode
Genome_build: Bos taurus genome build UMD3.1
Supplementary_files_format_and_content: txt files, raw read counts output from STAR alignment using option -–quantmode GeneCounts
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| Submission date |
Mar 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
James West |
| E-mail(s) |
j.west@vanderbilt.edu
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| Organization name |
Vanderbilt University
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| Department |
Medicine
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| Lab |
Allergy, Pulmonary and Critical Care
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| Street address |
4200 E 9TH Ave, Box B133
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| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37201 |
| Country |
USA |
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| Platform ID |
GPL21659 |
| Series (1) |
| GSE79659 |
Study of the impact of copper levels in bovine blood on transcriptional profile |
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| Relations |
| BioSample |
SAMN04588722 |
| SRA |
SRX1667247 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2100526_3355-SG-2ReadsPerGene.out.tab.gz |
162.0 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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