|
Status |
Public on Jun 04, 2020 |
Title |
SANDAWE4.TZSW193 |
Sample type |
SRA |
|
|
Source name |
blood
|
Organism |
Homo sapiens |
Characteristics |
tissue: blood ethnicity: SANDAWE subsistence: Former_Hunter-Gatherer
|
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 |
SAMN07197407 |
SRA |
SRX2885508 |