|
| Status |
Public on Dec 21, 2021 |
| Title |
19a_DMSO |
| Sample type |
SRA |
| |
|
| Source name |
Human macrophages (MO-GMCSF)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Macrophages (MO-GMCSF)
infection status: Infected with Mycobacterium tuberculosis
treatment: 0.2% DMSO
donor: 19a
|
| Treatment protocol |
MO-GMCSF were infected for 12 hours with Mycobacterium tuberculosis at MOI=1 (or left uninfected), then treated with the indicated compounds at 10 μM, 0.2% DMSO or plain media for 11 hours prior to lysis.
|
| Growth protocol |
Human primary monocytes were positively selected (CD14) from healthy donor peripheral blood mononuclear cells, then matured in 50 ng/mL GM-CSF for 6 days to create MO-GMCSF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with buffer RLT (Qiagen) and purified on Zymo columns with off-column DNA digestion.
Libraries were constructed using the KAPA mRNA HyperPrep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
mRNA
|
| Data processing |
Reads were aligned with STAR aligner (version 2.6.0) in the RSEM program (version 1.2.29).
RNAseq counts were analyzed in R (version 3.6.3) with DESeq2 (version 1.24.0).
During analysis in R, gene names were retrieved with biomaRt (version 2.40.5) and log2 fold-changes were shrunk with apeglm (version 1.6.0).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: SuppTable1-ext_RNAseq-Data-ext.xlsx: Raw counts are included in two sheets of the Excel document (one with and one without donor 18p counts); donors 18k, 18o, and 19a were used to calculate the log2 fold-changes and significance values in the other sheet.
|
| |
|
| Submission date |
Sep 10, 2021 |
| Last update date |
Dec 21, 2021 |
| Contact name |
Gregory Hunter Babunovic |
| E-mail(s) |
[email protected]
|
| Organization name |
Harvard T.H. Chan School of Public Health
|
| Department |
Immunology and Infectious Diseases
|
| Lab |
Sarah Fortune Lab
|
| Street address |
665 Huntington Ave., SPH 1, Room 802
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE183912 |
CRISPR interference reveals that all-trans-retinoic acid promotes macrophage control of Mycobacterium tuberculosis by limiting bacterial access to cholesterol and propionyl-CoA |
|
| Relations |
| BioSample |
SAMN21386056 |
| SRA |
SRX12132549 |
