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Sample GSM1426938 Query DataSets for GSM1426938
Status Public on Jul 04, 2014
Title TFOE_9265_3167c
Sample type RNA
 
Source name TFOE_9265_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 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-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

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

Data table
ID_REF VALUE
Rv0001 12.33513248
Rv0002 13.31707128
Rv0003 12.43539834
Rv0004 12.48018938
Rv0005 14.16737416
Rv0006 14.15553825
Rv0007 13.91395622
Rv0008c 11.73447189
Rv0009 14.44547782
Rv0010c 12.45557739
Rv0011c 13.39638238
Rv0012 12.98471439
Rv0013 12.31484402
Rv0014c 12.93667786
Rv0015c 13.09496048
Rv0016c 12.65832953
Rv0017c 13.07348322
Rv0018c 13.25666031
Rv0019c 13.35860629
Rv0020c 14.03371742

Total number of rows: 4026

Table truncated, full table size 76 Kbytes.




Supplementary file Size Download File type/resource
GSM1426938_TFOE_9265_3167c_N60A03cy3.xys.gz 711.0 Kb (ftp)(http) XYS
Processed data included within Sample table

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