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Sample GSM1905398 Query DataSets for GSM1905398
Status Public on Oct 10, 2015
Title sigW1.4_3
Sample type RNA
 
Channel 1
Source name wildtype
Organism Bacillus subtilis
Characteristics strain: PY79
genotype/variation: wildtype
Extracted molecule total RNA
Extraction protocol RNA was extracted using the Hot Phenol method followed by Dnase treatment and cleaning with Qiagen's Rneasy kit
RNA was extracted using the Hot Phenol method followed by Dnase treatment and cleaning with Qiagen's Rneasy kit
Label cy3
Label protocol 6-10 ug of RNA was labelled using Agilent's Fairplay III Protocol for NHS-ester dye-coupling reaction to amino allyl dUTP . Cy3 and Cy5 were purchased from GE Healthcare
6-10 ug of RNA was labelled using Agilent's Fairplay III Protocol for NHS-ester dye-coupling reaction to amino allyl dUTP . Cy3 and Cy5 were purchased from GE Healthcare
 
Channel 2
Source name sigW::erm
Organism Bacillus subtilis
Characteristics strain: PY79
genotype/variation: sigW::erm
Extracted molecule total RNA
Extraction protocol RNA was extracted using the Hot Phenol method followed by Dnase treatment and cleaning with Qiagen's Rneasy kit
RNA was extracted using the Hot Phenol method followed by Dnase treatment and cleaning with Qiagen's Rneasy kit
Label cy5
Label protocol 6-10 ug of RNA was labelled using Agilent's Fairplay III Protocol for NHS-ester dye-coupling reaction to amino allyl dUTP . Cy3 and Cy5 were purchased from GE Healthcare
6-10 ug of RNA was labelled using Agilent's Fairplay III Protocol for NHS-ester dye-coupling reaction to amino allyl dUTP . Cy3 and Cy5 were purchased from GE Healthcare
 
 
Hybridization protocol Hybridizations were incubated at 65˚C for 17 hours. After hybridization slides were washed using Agilent's Wash Buffer 1 and 2.
Hybridizations were incubated at 65˚C for 17 hours. After hybridization slides were washed using Agilent's Wash Buffer 1 and 2.
Scan protocol Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology
Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology
Description SigW regulon Replicate 3: A wild-type PY79 and PE2732 (sigW::erm) cultures were grown in parallel in Difco Sporulation Medium and samples were collected at OD600nm of 1.4.
Data processing Microarray data processing was performed in R (www.r-project.org) using the Bioconductor bioinformatics software package (www.bioconductor.org). Data were loaded into R using the marray package and normalized between arrays using loess normalization. Normalized log-ratios of gMedianSignal and rMedianSignal were collapsed for redundant probes taking the average.
Microarray data processing was performed in R (www.r-project.org) using the Bioconductor bioinformatics software package (www.bioconductor.org). Data were loaded into R using the marray package and normalized between arrays using loess normalization. Normalized log-ratios of gMedianSignal and rMedianSignal were collapsed for redundant probes taking the average.
 
Submission date Oct 09, 2015
Last update date Oct 10, 2015
Contact name Patrick Eichenberger
E-mail(s) [email protected], [email protected]
Organization name New York University
Department Center for Genomics and Systems Biology
Lab Eichenberger
Street address 12 Waverly Place
City New York
State/province New York
ZIP/Postal code 10003
Country USA
 
Platform ID GPL15179
Series (1)
GSE67023 An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network.

Data table header descriptions
ID_REF
VALUE normalized log2 ratio gMedianSignal/rMedianSignal

Data table
ID_REF VALUE
BSU00010 -0.467774889
BSU00020 -0.798710504
BSU00030 -0.652572125
BSU00040 -0.506978245
BSU00050 -0.546858711
BSU00060 -0.385128996
BSU00070 -0.476949718
BSU00080 -0.554009203
BSU00090 -1.048337656
BSU00100 -0.551277124
BSU00110 -0.596395851
BSU00120 -0.653540818
BSU00130 -0.328999906
BSU00140 -0.033822618
BSU00150 -0.076810023
BSU00160 -1.476647618
BSU00170 -1.347760632
BSU00180 0.010124913
BSU00190 -0.315226877
BSU00200 -0.152443918

Total number of rows: 4657

Table truncated, full table size 99 Kbytes.




Supplementary file Size Download File type/resource
GSM1905398_US93503718_252962910066_S01_GE2_107_Sep09_1_4.txt.gz 1.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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