|
| Status |
Public on May 06, 2019 |
| Title |
Whole blood sample from a healthy adult, 102037 |
| Sample type |
SRA |
| |
|
| Source name |
whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: whole blood
diagnosis: healthy
subject id: W070517102037
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from whole blood samples of 12 healthy adults stored in PAXgene tubes. RNA was isolated using the PAXgene Blood RNA Kit (Qiagen) according to the manufacturer’s recommendations. then quantitated and quality assessed using a 2100 Bioanalyzer (Agilent).
Library preparation was performed with the TruSeq RNA exome kit (Illumina) per the manufacturer’s recommendations. RNA-Seq libraries were multiplexed together and sequenced on a single HiSeq 4000 lane (Illumina) using 2 x 150bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
To maximize linearity in the context of deconvolution analyses, raw FASTQ reads were processed with Salmon v0.8.277 using GENCODE v23 reference transcripts, the –biasCorrect flag, and otherwise default parameters. RNA-Seq quantification results were merged into a single gene-level TPM matrix using the R package, tximport.
Genome_build: GENCODE v23
Supplementary_files_format_and_content: Gene expression matrix in TPM space, txt file
|
| |
|
| Submission date |
Mar 04, 2019 |
| Last update date |
May 06, 2019 |
| Contact name |
Aaron M Newman |
| E-mail(s) |
[email protected]
|
| Organization name |
Stanford University
|
| Department |
Institute for Stem Cell Biology and Regenerative Medicine, Department of Biomedical Data Science
|
| Lab |
Newman lab (http://anlab.stanford.edu)
|
| Street address |
265 Campus Drive
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE127472 |
High-throughput tissue dissection and cell purification with digital cytometry |
| GSE127813 |
High-throughput tissue dissection and cell purification with digital cytometry [healthy adults] |
|
| Relations |
| BioSample |
SAMN11051507 |
