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| Status |
Public on Oct 24, 2024 |
| Title |
THP-1 cells infected with rifampin-resistant H37Rv at 4 hours, biological replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Infected THP-1 cells (rifampin-resistant H37Rv, 4 hours)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Peripheral blood
cell line: THP-1
cell type: Monocytic cell line
infection: rifampin-resistant H37Rv
time: 4 hours
|
| Biomaterial provider |
ATCC Catalog no. TIB-202
|
| Treatment protocol |
THP-1 cells were differentiated for 48 hours with 10 ng/ml PMA prior to infection with four different reference Mycobacterium tuberculosis (drug-sensitive H37Ra, drug-sensitive H37Rv, isoniazid-resistant H37Rv, rifampin-resistant H37Rv). Two time points, 4 hours and 24 hours, were used for infecting the cells. We also included control non-infected cells (mock-infected with PBS) as negative controls.
|
| Growth protocol |
THP-1 cells were maintained in RPMI 1640 medium supplemented with 10% heat-inactivated FBS at 37∘C and 5% CO2 in a humidified incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from control and infected cells using Trizol, according to the manufacturer's protocol.
|
| Label |
Biotin
|
| Label protocol |
Total RNA was reverse-transcribed to cDNA, amplified and labeled, according to the standard Affymetrix instructions.
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| |
|
| Hybridization protocol |
Samples were hybridized to separate arrays using the GeneChip Human Exon 1.0 ST Array, according to the manufacturer's instructions. Triplicate hybridization assays were performed in these microarray experiments.
|
| Scan protocol |
Quality control of the hybridized arrays was carried out for each sample. A visual inspection of the scanned images was conducted looking for any defects, areas of high background, or areas of low signal. The spike-in controls were checked as well to examine for hybridization uniformity.
|
| Description |
Gene expression data from THP-1 cells infected with a rifampin-resistant H37Rv Mycobacterium tuberculosis strain at 4 hours.
|
| Data processing |
Data from all samples were preprocessed, summarized at the transcript-cluster (gene) level and RMA normalized using Affymetrix Power tools. Differential expression analyses were conducted using the R/Bioconductor package limma.
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| |
|
| Submission date |
Nov 01, 2023 |
| Last update date |
Oct 24, 2024 |
| Contact name |
Loubna Tazi |
| E-mail(s) |
[email protected]
|
| Phone |
530-752-7807
|
| Organization name |
UC Davis School of Medicine
|
| Department |
Medical Microbiology & Immunology
|
| Street address |
451 Health Science Drive
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL5175 |
| Series (1) |
| GSE246736 |
Gene expression data from THP-1 cells infected with different Mycobacterium tuberculosis strains |
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