|
| Status |
Public on Nov 26, 2021 |
| Title |
HMN171223_12hr |
| Sample type |
SRA |
| |
|
| Source name |
PBMCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: peripheral blood mononuclear cells
treatment: flu-infected
|
| Treatment protocol |
Per individual for each condition, 1 million (M) PBMCs were plated at a concentration of 1M/ml and infected with either mock-conditioned media (negative control) or Cal/04/09 IAV at an MOI of 0.5. After 30 minutes of IAV infection, the virus was washed from PBMC cultures, cells were replated, and cells were then incubated for various time points at 37C in 5% CO2 and 20% O2.
|
| Growth protocol |
All samples were obtained from BioIVT. Blood was collected utilizing a standard protocol from 90 male African- (AFR) and European-American (EUR) donors between the ages of 21 – 69 using a sodium heparin anticoagulant from the same collection site in the United States. A signed, written consent was obtained from each participant. Briefly, PBMCs were extracted from whole blood using a density gradient, washed with HBSS, reconstituted in CryoStor CS10 to a concentration of 10 million (M) cells/ml, and subsequently cryopreserved.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were collected, washed, and stored in Qiazol prior to RNA extraction.
RNA libraries were prepared for sequencing using TM3’seq, a 3’-enriched library preparation protocol (https://www.g3journal.org/content/10/1/143).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
bulk RNA library
time_course_PBMCs.Homo_sapiens_with_flu.GRCh38.kallisto.gene_level.ScaledTPM.txt
|
| Data processing |
Fastqs were trimmed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) in single-end mode (-q 20 --phred33)
Reads were pseudoaligned to GRCh38 and the IAV reference transcriptome using kallisto's quant function (Bray et al.) in single-end mode
Quantification estimates were obtained from abundance.h5 files using the R package tximport (Soneson et al.)
Genome_build: GRCh38.p12 and influenza A virus (A/California/04/09)
Supplementary_files_format_and_content: time_course_PBMCs.Homo_sapiens_with_flu.GRCh38.kallisto.gene_level.ScaledTPM.txt includes counts from abundance estimates scaled by library size
|
| |
|
| Submission date |
Mar 08, 2021 |
| Last update date |
Nov 26, 2021 |
| Contact name |
Luis B Barreiro |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Chicago
|
| Lab |
Barreiro Lab
|
| Street address |
900 E 57th Street
|
| City |
Chicago |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE162632 |
Single-cell RNA-sequencing reveals pervasive but highly cell type-specific genetic ancestry effects on the response to viral infection |
|
| Relations |
| BioSample |
SAMN18214415 |
| SRA |
SRX10279351 |
