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Sample GSM1084393 Query DataSets for GSM1084393
Status Public on Feb 19, 2013
Title Rv0117 OE by ATc 100 ng Atc 18 Hours TFOE_1280_0117
Sample type RNA
 
Source name TFOE_1280_0117
Organism Mycobacterium tuberculosis H37Rv
Characteristics experiment: Rv0117
replicate: A
time: 18 Hours
dose: 100 ng Atc
treatment: Rv0117 OE by ATc
Treatment protocol TFOE experiments done at indicated concentration of anhydrotetracycline. Hypoxic experiments conducted as described previously (Rustad et al., 2008)
Growth protocol H37Rv was grown to log phase (0.1-0.5 OD600) in Middlebrook 7H9 media supplemented with ADC (Difco) at 37C.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).
Label cy3
Label protocol Labeling was performed using indirect labelling of amino-allyl dUTP using protocol from PFGRC (www.pfgrc.org).
 
Hybridization protocol Hybridization was performed following the standard operating protocol recommended by NimbleGen Systems Inc., Madison, WI, USA . See www.nimblegen.com.
Scan protocol Scanning was performed using a GenePix 4000B using a single intensity for all 12 arrays on each slide.
Description TFOE_1280_0117
Rv0117 OE by ATc
18
Hours
100
ng
Data processing Data was normalized using RMA normalization with the 'affy' package for R.
 
Submission date Feb 19, 2013
Last update date May 13, 2015
Contact name Tige Rustad
E-mail(s) tige.rustad@sbri.org
Phone 206-256-7207
Organization name Seattle Biomedical Research Institute
Department Pathobiology
Lab Sherman
Street address 307 Westlake Avenue N, Suite 500
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL14824
Series (1)
GSE43466 Reconstruction of the Mycobacterium tuberculosis Regulatory Network and Deconstruction of the Hypoxic Response
Relations
Reanalyzed by GSM1426406

Data table header descriptions
ID_REF
VALUE RMA normalized expression (log2 values)

Data table
ID_REF VALUE
Rv0001 12.56979297
Rv0002 13.23213119
Rv0003 12.13216633
Rv0004 11.89563732
Rv0005 12.90586767
Rv0006 13.1940815
Rv0007 13.07517964
Rv0008c 10.4006702
Rv0009 13.3715808
Rv0010c 11.55799325
Rv0011c 12.38467699
Rv0012 11.74360533
Rv0013 11.25853014
Rv0014c 12.10660806
Rv0015c 11.93772196
Rv0016c 11.65163572
Rv0017c 12.07370791
Rv0018c 12.04379613
Rv0019c 12.13465077
Rv0020c 12.92815925

Total number of rows: 4026

Table truncated, full table size 76 Kbytes.




Supplementary file Size Download File type/resource
GSM1084393_TFOE_1280_0117_N03A04cy3.pair.gz 2.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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