|
| Status |
Public on Mar 10, 2015 |
| Title |
CTRL, 2961-TA-43 |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral whole blood draw, healthy control
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral whole blood
disease state: healthy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral whole blood was collected into PaxGene tubes. RNA was isolated per the manufacturer's supplied protocol.
Total RNA isolated from PaxGene tubes was purified with the RNeasy MinElute Cleanup kit (Qiagen) using an on-column DNase treatment to ensure absence of genomic DNA contamination according to the manufacturer’s supplied protocol.
2343 and 2961 libraries were constructed using the Illumina TruSeq Stranded mRNA kit (Cat. No. RS-122-2101) following the manufacturer's supplied protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Quality control to filter out bad samples and reads.
Alignment to human genome (hg19) using TopHat 2.
Read count quantification using HTSeq.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text file includes FPKMs.
|
| |
|
| Submission date |
Mar 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Charles F Spurlock III |
| E-mail(s) |
chase.spurlock@vanderbilt.edu
|
| Phone |
6153432363
|
| Organization name |
Vanderbilt University School of Medicine
|
| Department |
Medicine
|
| Lab |
T3113
|
| Street address |
1161 21st Avenue South
|
| City |
Nashville |
| State/province |
Tennessee |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE66573 |
Defective structural RNA processing in relapsing-remitting multiple sclerosis |
|
| Relations |
| BioSample |
SAMN03389441 |
| SRA |
SRX902284 |
