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Sample GSM734336 Query DataSets for GSM734336
Status Public on Dec 01, 2011
Title THP1-cells infected by H37Rv strains at 48h, Replication 2
Sample type RNA
 
Source name THP1-cells infected by H37Rv strains at 48h, Replication 2
Organism Homo sapiens
Characteristics cell line: THP-1 cells
m. tuberculosis strain: H37Rv
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 H37Rv strains at 48h, Replication 2
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 6.272583
1053_at 6.325116
117_at 7.101638
121_at 7.169865
1255_g_at 2.212574
1294_at 7.486636
1316_at 3.874994
1320_at 3.263186
1405_i_at 12.46988
1431_at 2.496929
1438_at 4.358192
1487_at 7.517226
1494_f_at 5.183004
1552256_a_at 6.648878
1552257_a_at 7.147996
1552258_at 3.43335
1552261_at 2.825788
1552263_at 6.396698
1552264_a_at 7.535042
1552266_at 2.368981

Total number of rows: 54675

Table truncated, full table size 1053 Kbytes.




Supplementary file Size Download File type/resource
GSM734336.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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