|
| Status |
Public on Dec 01, 2011 |
| Title |
THP1-cells infected by 19.5 strains at 48h |
| Sample type |
RNA |
| |
|
| Source name |
THP1-cells infected by 19.5 strains at 48h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP-1 cells
m. tuberculosis strain: R19.5
infection time: 48h
|
| Growth protocol |
M. tuberculosis strains were grown in Middlebrook 7H9 broth (BD Difco) supplemented with 10 % of albumin-dextrose-catalase (OADC) enrichment and 0.05 % tween 80 at 37°C with shaking at 100 rpm. Bacteria were cultured until exponential phase, then aliquoted and frozen at -80℃. THP-1 cells was maintained at 37°C in 5% CO2 in RPMI 1640 media (Life Technologies) supplemented with 10% of FBS. Prior to infection, THP-1 cells were differentiated into macrophage-like cells in T-75 flasks (1×107 cells/flask) with 200nM phorbol myristate acetate (PMA, Sigma-Aldrich) for 24h followed by incubation with fresh media without PMA for 24h. At time points of 4h, 18h and 48h, cell were lysed with 2 ml of Trizol (Life Technologies) for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
The biotinylated cRNA was then fragmented and subjected to hybridization on Human Genome U133 Plus 2.0 Array (Affymetrix, USA).
|
| Scan protocol |
An affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays
|
| Description |
THP1-cells infected by 19.5 strains at 48h
|
| Data processing |
These CEL raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization in R (Bioconductor)
|
| |
|
| Submission date |
May 31, 2011 |
| Last update date |
Dec 01, 2011 |
| Contact name |
Hai Fang |
| E-mail(s) |
hfang@cs.bris.ac.uk
|
| Organization name |
University of Bristol
|
| Department |
Department of Computer Science
|
| Street address |
Woodland Road
|
| City |
Bristol |
| ZIP/Postal code |
BS8 1UB |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE29628 |
The time-course transcriptomic responses of THP-1 human macrophage-like cells to W-Beijing Mycobacterium tuberculosis strains of different sublineages |
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