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Sample GSM678274 Query DataSets for GSM678274
Status Public on Feb 22, 2011
Title phoB mutant_6.6mM
Sample type RNA
 
Source name Bacteroides fragilis
Organism Bacteroides fragilis
Characteristics strain: TCSM1576
genotype/variation: BF1576 (phoB) mutant
culture condition: Pi-excess (6.6mM Pi) condition
Growth protocol Bacteroides fragilis strains were grown to mid-log phase (O.D.600nm 0.4-0.6) in defined minimal media (Varel, V.H et al. Appl. Microbiol.28(2):251-257, 1974.) supplemented with 6.6 mM or 0.0066 mM of KH2PO4.
Extracted molecule total RNA
Extraction protocol Total RNAs were extracted using hot-phenol method.
Label Cy3
Label protocol Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Description delta PhoB 6.6
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis), quantile normalization, and background correction as implemented in the ArrayStar software (DNASTAR)
 
Submission date Feb 22, 2011
Last update date Feb 22, 2011
Contact name Haruyuki Nakayama-Imaohji
E-mail(s) nakayama@basic.med.tokushima-u.ac.jp
Organization name Tokushima University
Street address 3-18-15 kuramoto-cho
City tokushima
ZIP/Postal code 770-8503
Country Japan
 
Platform ID GPL13213
Series (1)
GSE27439 Identification of the regulatory circuit of PhoB in Bacteroides fragilis strain YCH46

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
TI295405P00000001 24.93
TI295405P00000002 180.83
TI295405P00000003 945.40
TI295405P00000004 1513.48
TI295405P00000005 1869.72
TI295405P00000006 3048.54
TI295405P00000007 4354.67
TI295405P00000008 16227.43
TI295405P00000009 13621.45
TI295405P00000010 6525.87
TI295405P00000011 2849.39
TI295405P00000012 3568.04
TI295405P00000013 6491.37
TI295405P00000014 5766.84
TI295405P00000015 4320.70
TI295405P00000016 4842.45
TI295405P00000017 2738.25
TI295405P00000018 8394.28
TI295405P00000019 5531.48
TI295405P00000020 1303.06

Total number of rows: 4527

Table truncated, full table size 111 Kbytes.




Supplementary file Size Download File type/resource
GSM678274_45775702_532.calls.gz 338.8 Kb (ftp)(http) CALLS
GSM678274_45775702_532.pair.gz 1.0 Mb (ftp)(http) PAIR
GSM678274_45775702_532_RMA.calls.gz 49.1 Kb (ftp)(http) CALLS
GSM678274_45775702_532_norm_RMA.pair.gz 1.0 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file
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