|
| Status |
Public on Aug 09, 2020 |
| Title |
PTM_4X0429_LPS24 |
| Sample type |
SRA |
| |
|
| Source name |
Chimp whole blood stimulation
|
| Organism |
Pan troglodytes |
| Characteristics |
tissue: whole blood
treatment: LPS
time points: 24
Sex: M
individual id: 4X0429
|
| Treatment protocol |
TruCulture tubes + species blood were incubated for 4 and 24 hours time points
|
| Growth protocol |
1 ml of species blood was incubated in Truculture tube pre prepared with stimulant (lipopolysaccharide or gardiquimod) or negative control (endotoxin-free water)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RBC lysis and RNA extraction of total white blood cells was carried out after stimulation
Messenger RNA (mRNA) was 491 isolated by magnetic bead and converted into RNA libraries using the Illumina TruSeq RNA 492 Library preparation kit v2 according to the manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were trimmed from Illumina adapter sequence from the ends of the reads and remove bases with quality scores < 20
STAR software was used to align the reads to reference genomes
Gene expression estimates were obtained by summing the number of reads that mapped uniquely to each species annotated genome using HTSeq-count
Genome_build: hg19 for human; CHIMP2.1.4 for chimpanzee; MMUL 1.0 for macaque; PapAnu2.0 for olive baboon species.
Supplementary_files_format_and_content: cram files of aligned reads to species genomes
|
| |
|
| Submission date |
Aug 08, 2020 |
| Last update date |
Aug 09, 2020 |
| Contact name |
Luis B Barreiro |
| E-mail(s) |
lbarreiro@uchicago.edu
|
| Organization name |
Chicago University
|
| Department |
Genetic Medicine
|
| Lab |
Barreiro Lab
|
| Street address |
900 East 57th Street
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL16809 |
| Series (1) |
| GSE155918 |
Primate innate immune responses to bacterial and viral pathogens reveals an evolutionary trade-off between strength and specificity |
|
| Relations |
| BioSample |
SAMN15767829 |
| SRA |
SRX8912108 |
