|
| Status |
Public on Oct 20, 2016 |
| Title |
risk (CC) (sample 57) |
| Sample type |
SRA |
| |
|
| Source name |
PBMCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: EBV (Epstein Barr Virus)-transformed B lymphocyte cells
genotype: (CC)
|
| Growth protocol |
Cells were maintained in RPMI and the media was changed every third day.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from EBV (Epstein Barr Virus)-transformed B lymphocyte cells, from 3 carriers of the risk (CC) allele and 3 non-carriers of the (GG) reference allele, was isolated using the Qiagen RNeasy-Midi kit (Cat#75142). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
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 |
| |
|
| Data processing |
Perkin Elmer's Genesifter Analysis Edition Software
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Human Build 37.2 using BWA.
Raw read count was normalized by total mapped million reads (RPM).
Benjamini-Hochberg correction
Genome_build: 37.2
Supplementary_files_format_and_content: Excel files include raw and RPM values for combined triplicate samples.
|
| |
|
| Submission date |
Oct 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Annabelle Rodriguez |
| E-mail(s) |
rodriguezoquendo@uchc.edu
|
| Phone |
(860) 679-2463
|
| Organization name |
UCONN Health
|
| Department |
Center for Vascular Biology
|
| Lab |
Rodriguez
|
| Street address |
263 Famington Ave, MC-3501
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06030-3501 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE87891 |
Lymphocyte activation gene3 and coronary artery disease. |
|
| Relations |
| BioSample |
SAMN05901242 |
| SRA |
SRX2241075 |
