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Sample GSM734337 Query DataSets for GSM734337
Status Public on Dec 01, 2011
Title THP1-cells infected by MAD2.2 strains at 4h
Sample type RNA
 
Source name THP1-cells infected by MAD2.2 strains at 4h
Organism Homo sapiens
Characteristics cell line: THP-1 cells
m. tuberculosis strain: MAD2.2
infection time: 4h
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 MAD2.2 strains at 4h
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

Data table header descriptions
ID_REF
VALUE RMA-normalized signal intensity

Data table
ID_REF VALUE
1007_s_at 6.593452
1053_at 6.810626
117_at 4.768987
121_at 6.881753
1255_g_at 2.244972
1294_at 6.42384
1316_at 3.324193
1320_at 3.35193
1405_i_at 11.109443
1431_at 2.639206
1438_at 4.281587
1487_at 7.325042
1494_f_at 4.989754
1552256_a_at 7.293999
1552257_a_at 7.258983
1552258_at 3.216877
1552261_at 2.991606
1552263_at 6.050579
1552264_a_at 8.030954
1552266_at 2.278051

Total number of rows: 54675

Table truncated, full table size 1053 Kbytes.




Supplementary file Size Download File type/resource
GSM734337.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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