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Sample GSM3070839 Query DataSets for GSM3070839
Status Public on Oct 09, 2018
Title bmj21D
Sample type RNA
 
Source name cDNA prepared from dark culture of B. multivorans in middle stationary phase
Organism Burkholderia multivorans
Characteristics strain: ATCC 17616
growth phase: middle stationary
light status: dark culture
Growth protocol B. multivorans ATCC 17616 strain was grown in LB at 28°C at 135 strokes/min for 14 or 21 hrs under dark and light conditions.
Extracted molecule total RNA
Extraction protocol Cells were treated with RNA Protect Bacteria reagent (Qiagen, CA, USA). Total RNA was extracted using RNeasy Midi kit (Qiagen).
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 This sample is of wild-type Burkholderia multivorans cultured under the dark condition for 21 h.
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
 
Submission date Mar 28, 2018
Last update date Oct 09, 2018
Contact name Hideaki Takano
E-mail(s) takano.hideaki@nihon-u.ac.jp
Phone 81466843936
Organization name Nihon University
Department College of Bioresource Sciences
Street address 1866, Kameino
City Fujisawa
State/province KANAGAWA
ZIP/Postal code 2520880
Country Japan
 
Platform ID GPL24783
Series (1)
GSE112472 Role and function of Class III LitR, a photosensor homolog from Burkholderia multivorans ATCC 17616 in the regulation of folate production.

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

Data table
ID_REF VALUE
BMULJ_00001 2154
BMULJ_00002 2701
BMULJ_00003 69
BMULJ_00004 9624
BMULJ_00005 122
BMULJ_00006 1344
BMULJ_00007 666
BMULJ_00008 107
BMULJ_00009 67
BMULJ_00010 180
BMULJ_00011 2310
BMULJ_00012 46
BMULJ_00013 46
BMULJ_00014 39
BMULJ_00015 43
BMULJ_00016 146
BMULJ_00017 220
BMULJ_00018 69
BMULJ_00019 144
BMULJ_00020 747

Total number of rows: 5981

Table truncated, full table size 94 Kbytes.




Supplementary file Size Download File type/resource
GSM3070839_421301A02_532.pair.gz 33.5 Kb (ftp)(http) PAIR
GSM3070839_421301A02_532_norm_RMA.pair.gz 1.1 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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