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Sample GSM1826420 Query DataSets for GSM1826420
Status Public on Jul 18, 2016
Title Bacillus subtilis_Temp_normal_rep3
Sample type RNA
 
Source name Bacillus subtilis, normaltemperature fermentation,replicate 3
Organism Bacillus subtilis
Characteristics culture time: 48h
Treatment protocol The sample of BS_A1, BS_A2, BS_A3, BS_A4 were cultuered according to the workflow below: culturing at 37℃ for 12 hours, then taking it into 46℃ for 12 hours. It continued to culturing at 55℃ for 24 hours in the final step. The sample of BS_B1,BS_B2,BS_B3,BS_B4 were cultured at 37℃ in the whole 48 hours.
Growth protocol A wort agar medium including a quarter of beef extract peptone was used to Bacillus subtilis fermentation for 48 hours. The seed of B.subtilis was prepared in the Luria-Bertani medium at 37℃ overnight.
Extracted molecule total RNA
Extraction protocol A modified CTAB method was used for total RNA extraction. The ingredient of the CTAB extraction liquid including 2% CTAB, 30mmol/L EDTA, 2mol/L NaCl, 100mmol/L Tris-HCl, pH 8.0,0.05% spermidine. adding the reagents in a clean RNase-free 1.5 ml centrifugal tube (including 600 L CTAB extraction liquid, 12 µL 2% PVP, 12 ul mercaptoethanol and final concentration of 1.5 mg/ml of proteinase K, 42 ℃ incubation for 10 minutes.Then transferred it to the sample tube and added 100 ul lysozyme (1 mg/ml), vortex oscillation, 42 ℃ incubation 90min ( vortexing several times during the time).For cell lysis nucleic acid substances released after the separation and purification of RNA as follows: in the previous step sample tube with equal volume of chloroform, isoamyl alcohol, vortex, 13000 rpm, 4 ℃ centrifuge for 15 min.Transfered the upper water phase to a new tube, repeating the above steps.Add precooling the solution (volume of 4 m LiCl and 1/2 volume of anhydrous ethanol) to the previous upper water. Precipitating the nucleic acid on ice for 3 hours. the pellets was ultraclean using 600 ul - 800 ul 2M LiCl and 75% ethanol.Obtaining total RNA.by add approprate amount DEPC water dissolved the pellets .
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol not provided
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Description BS_B3
gene experssion at a normal temperature
Data processing The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Jul 17, 2015
Last update date Jul 18, 2016
Contact name weiying wang
E-mail(s) windowandme@163.com
Phone 13770769131
Organization name Nanjing Normal University
Department College of Life Sciences
Street address 1 Wenyuan Road
City Nanjing
ZIP/Postal code 210046
Country China
 
Platform ID GPL20709
Series (1)
GSE71067 The gene expression profile of Bacillus subtilis response to the high-temperature fermentation

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
CUST_2400_PI429823780 4.7988687
CUST_1702_PI429823780 4.782124
CUST_5372_PI429823780 4.78513
CUST_129_PI429823780 4.674585
CUST_1016_PI429823780 4.7331977
CUST_5695_PI429823780 4.7362127
CUST_5489_PI429823780 4.6728306
CUST_470_PI429823780 4.621179
CUST_4939_PI429823780 4.75134
CUST_4366_PI429823780 4.77233
CUST_3456_PI429823780 4.67758
CUST_3711_PI429823780 4.6860123
CUST_452_PI429823780 4.6464415
CUST_6438_PI429823780 4.626933
CUST_616_PI429823780 4.673671
CUST_2671_PI429823780 4.656733
CUST_5776_PI429823780 4.6254773
CUST_5564_PI429823780 4.6078067
CUST_3968_PI429823780 4.6703763
CUST_6520_PI429823780 4.649942

Total number of rows: 6825

Table truncated, full table size 207 Kbytes.




Supplementary file Size Download File type/resource
GSM1826420_B3.txt.gz 4.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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