|
| Status |
Public on Jun 04, 2020 |
| Title |
AMHARA4.ETAM052 |
| Sample type |
SRA |
| |
|
| Source name |
blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
ethnicity: AMHARA
subsistence: Agriculturalist
|
| Treatment protocol |
PBMCs collected on Ambion LeukoLOCK filters bathed in RNAlater and frozen at -80 degrees
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole blood, modified Trizol/ Cartridge isolation from Ambion.
Poly(A) selection by MicroPoly(A) Purist Kit AM1919 from Ambion.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
CASAVA (v1.8.1) was used to demultiplex pooled samples and convert BCL to FASTQ.
RNA-Seq data were aligned to the human genome build hg19 by STAR-2.5.1b.
Data were normalized at the gene-level, using a resampling strategy PORT (v0.8.1-beta), the code is available at https://github.com/itmat/Normalization
Genome_build: hg19 (ensemblv75)
Supplementary_files_format_and_content: tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.
|
| |
|
| Submission date |
Jun 06, 2017 |
| Last update date |
Jun 04, 2020 |
| Contact name |
Gregory Robert Grant |
| E-mail(s) |
ggrant@upenn.edu
|
| Phone |
215-573-3736
|
| Organization name |
University of Pennsylvania
|
| Department |
Genetics
|
| Lab |
ITMAT Bioinformatics
|
| Street address |
3400 Civic Center Blvd.
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE99719 |
Transcriptome Diversity Associated with Ancestry and Diet in Ethnically Diverse East African Populations |
|
| Relations |
| BioSample |
SAMN07197403 |
| SRA |
SRX2885497 |
