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Sample GSM1426404 Query DataSets for GSM1426404
Status Public on Jul 04, 2014
Title TFOE_7211_0081_2B
Sample type RNA
 
Source name TFOE_7211_0081_2B
Organism Mycobacterium tuberculosis H37Rv
Characteristics experiment: Rv0081
stress: Rv0081 overexpression
time (hours): 18
concentration (ng): 100
Treatment protocol Transcription factor overexpression experiments done at 100 ng/ml of anhydrotetracycline after 18 hours of induction.
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 H37RvC:pEXCF-0081
Data processing Data was normalized using RMA normalization with the 'affy' package for R.
 
Submission date Jul 03, 2014
Last update date Jul 04, 2014
Contact name Tige Rustad
E-mail(s) trustad@gmail.com
Organization name Seattle BioMed
Lab Sherman
Street address 1700 DAYTON AVE NE
City RENTON
State/province WASHINGTON
ZIP/Postal code 98056
Country USA
 
Platform ID GPL14824
Series (1)
GSE59086 Mapping and manipulating the M. tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network
Relations
Reanalysis of GSM1084478

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

Data table
ID_REF VALUE
Rv0001 13.36457614
Rv0002 13.72287196
Rv0003 12.49079872
Rv0004 12.45527206
Rv0005 14.36474231
Rv0006 14.08761834
Rv0007 13.79518282
Rv0008c 11.99949214
Rv0009 14.56774541
Rv0010c 12.71434077
Rv0011c 13.88764677
Rv0012 12.99077319
Rv0013 12.61216962
Rv0014c 12.91066396
Rv0015c 12.33526232
Rv0016c 12.5062928
Rv0017c 13.11284087
Rv0018c 12.90684648
Rv0019c 12.9057198
Rv0020c 13.60851169

Total number of rows: 4026

Table truncated, full table size 76 Kbytes.




Supplementary file Size Download File type/resource
GSM1426404_TFOE_7211_0081_2B_N6A08cy3.xys.gz 700.9 Kb (ftp)(http) XYS
Processed data included within Sample table

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