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Sample GSM1426936 Query DataSets for GSM1426936
Status Public on Jul 04, 2014
Title TFOE_5913_3167c
Sample type RNA
 
Source name TFOE_5913_3167c
Organism Mycobacterium tuberculosis H37Rv
Characteristics experiment: Rv3167c
stress: Rv3167c 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 Cy5
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-3167c
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 GSM1084459

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

Data table
ID_REF VALUE
Rv0001 12.987875
Rv0002 13.21549331
Rv0003 12.81326568
Rv0004 12.82262766
Rv0005 14.38789726
Rv0006 14.22624156
Rv0007 14.01906993
Rv0008c 11.49483715
Rv0009 14.35902283
Rv0010c 12.4286243
Rv0011c 14.06312848
Rv0012 12.89901076
Rv0013 12.51555653
Rv0014c 13.33895074
Rv0015c 13.38516
Rv0016c 12.76014807
Rv0017c 13.20235886
Rv0018c 13.28192303
Rv0019c 13.2673474
Rv0020c 13.90096167

Total number of rows: 4026

Table truncated, full table size 76 Kbytes.




Supplementary file Size Download File type/resource
GSM1426936_TFOE_5913_3167c_N6A03cy5.xys.gz 698.6 Kb (ftp)(http) XYS
Processed data included within Sample table

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