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Sample GSM1130094 Query DataSets for GSM1130094
Status Public on Apr 27, 2013
Title SS_A2_d3263.3
Sample type RNA
 
Source name Rv3263 deletion mutant replicate 3
Organism Mycobacterium tuberculosis H37Rv
Characteristics strain: H37Rv
genotype: deltaRv3263
Growth protocol Cultures were grown to OD 0.8-0.9 in 7H9 supplemented with OADC, 0.05% Tween-80, and 0.2% glycerol in roller bottles
Extracted molecule total RNA
Extraction protocol Cultures were inactivated with RNAlater, disrupted with bead-beating in the presence of Trizol, and total RNA was extracted according to the manufacturer's instructions. RNA was then treated with Dnase and re-purified with RNeasy.
Label biotin
Label protocol Standard Affymetrix protocol for prokaryotic microarrays
 
Hybridization protocol Affymetrix protocol recommended for Pseudomonas aeruginosa
Scan protocol Microarrays were scanned using Affymetrix GeneArray Scanner 3000 7G Plus according to the manufacturer's protocol.
Description Gene expression data from an M. tuberculosis methyltransferase deletion mutant
Data processing Gene expression estimates were derived from the probe-level hybridization intensities using the RMA algorithm through the Expression Console software package (Affymetrix) using library files obtained from the array manufacturer (Affymetrix).
 
Submission date Apr 26, 2013
Last update date Apr 29, 2013
Contact name Scarlet Shell
E-mail(s) sshell@wpi.edu
Organization name Worcester Polytechnic Institute
Department Biology and Biotechnology
Lab Scarlet Shell
Street address 60 Prescott St
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
 
Platform ID GPL17082
Series (1)
GSE46432 Analysis of the effects of the methyltransferase encoded by Rv3263 on gene expression in M. tuberculosis

Data table header descriptions
ID_REF
VALUE log2-transformed, RMA-normalized Affymetrix probeset expression values

Data table
ID_REF VALUE
Rv3263_at 5.042568
TBID_IG_02927_at 13.0941
TBID_IG_02925_st 11.63982
Rv2463_at 12.11165
TBID_IG_03830_at 9.647305
TBID_IG_02928_st 13.33304
TBID_IG_03832_at 10.82308
TBID_IG_02926_at 11.3707
TBID_IG_03834_st 8.542521
MTB000055_at 10.69243
TBID_IG_03831_st 10.86886
TBID_IG_03829_st 9.548512
Rv0142_at 7.598665
TBID_IG_03832_st 10.44495
TBID_IG_00137_at 9.752201
TBID_IG_00138_st 9.498246
TBID_IG_03833_at 8.143297
TBID_IG_03753_st 9.944935
Rv0093c_at 8.466587
TBID_IG_03754_at 10.06601

Total number of rows: 13284

Table truncated, full table size 310 Kbytes.




Supplementary file Size Download File type/resource
GSM1130094_SS_A8_d3263-3.CEL.gz 991.2 Kb (ftp)(http) CEL
Processed data included within Sample table

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