|
| Status |
Public on Jun 10, 2014 |
| Title |
case_1 |
| Sample type |
SRA |
| |
|
| Source name |
coronary artery calcification case
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
ancestry: Caucasian
age (yrs): 55
sample group: coronary artery calcification case
tissue: peripheral blood
|
| Extracted molecule |
total RNA |
| Extraction protocol |
2.5 ml of peripheral blood was drawn into PAXgene RNA tubes and RNA extraction was done using the PAXgene Blood RNA Kit IVD (Qiagen). RNA-Seq libraries were constructed from 1 µg of RNA
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
163383
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were aligned using TopHat v1.0.14 with the parameters -m 2 -p 4 -g 10
The TopHat output SAM files were converted to BAM files using samtools view -T
The BAM files were converted to BED format using the bamToBed script from the BEDTools suite using the -split option
The BED files were converted to WIG format using a custom script
Genome_build: hg18
Supplementary_files_format_and_content: UCSC WIG format files containing RNA-Seq expression
|
| |
|
| Submission date |
Jun 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Shurjo Kumar Sen |
| E-mail(s) |
sensh@mail.nih.gov
|
| Organization name |
NHGRI
|
| Street address |
10 Center Drive, Room 7N317
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE58150 |
Integrative DNA, RNA and protein evidence connects TREML4 to coronary artery calcification |
|
| Relations |
| BioSample |
SAMN02821184 |
| SRA |
SRX559927 |
