NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM678275 Query DataSets for GSM678275
Status Public on Feb 22, 2011
Title phoB mutant_0.0066mM
Sample type RNA
 
Source name Bacteroides fragilis
Organism Bacteroides fragilis
Characteristics strain: TCSM1576
genotype/variation: BF1576 (phoB) mutant
culture condition: Pi-limiting (0.0066mM 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 0.006
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 19.25
TI295405P00000002 571.32
TI295405P00000003 2256.75
TI295405P00000004 756.50
TI295405P00000005 517.10
TI295405P00000006 581.58
TI295405P00000007 602.06
TI295405P00000008 3117.70
TI295405P00000009 3787.91
TI295405P00000010 976.00
TI295405P00000011 348.89
TI295405P00000012 427.54
TI295405P00000013 1086.42
TI295405P00000014 954.74
TI295405P00000015 610.50
TI295405P00000016 851.55
TI295405P00000017 355.21
TI295405P00000018 1604.86
TI295405P00000019 831.51
TI295405P00000020 164.94

Total number of rows: 4527

Table truncated, full table size 111 Kbytes.




Supplementary file Size Download File type/resource
GSM678275_45776002_532.calls.gz 339.1 Kb (ftp)(http) CALLS
GSM678275_45776002_532.pair.gz 1.0 Mb (ftp)(http) PAIR
GSM678275_45776002_532_RMA.calls.gz 49.3 Kb (ftp)(http) CALLS
GSM678275_45776002_532_norm_RMA.pair.gz 1.0 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap