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Sample GSM662993 Query DataSets for GSM662993
Status Public on May 08, 2014
Title _3_Cy3 (HX12)
Sample type RNA
 
Source name T2
Organism Acetivibrio thermocellus ATCC 27405
Characteristics time point: T2
array: 9
Growth protocol Batch fermentations were conducted in approximately 5 L of MTC medium with switchgrass as carbon source as described previously (Yang et al., 2008).
Extracted molecule total RNA
Extraction protocol RNA was isolated essentially described previously (Yang et al. 2010. PNAS. 107:10395–10400). Briefly, samples were harvested by centrifugation and the TRIzol reagent (Invitrogen, Carlsbad, CA) was used to extract total cellular RNA. Each total RNA preparation was treated with RNase-free DNase I (Ambion, Austin, TX) to digest residual chromosomal DNA and subsequently purified with the Qiagen RNeasy Mini kit in accordance with the instructions from the manufacturer. Total cellular RNA was quantified at OD260 and OD280 with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the RNA quality was checked with Agilent Bioanalyzer (Agilent, CA). The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).
Label Cy3
Label protocol The labeling, hybridization, and scanning following NimbleGen company's protocols.
 
Hybridization protocol The labeling, hybridization, and scanning following NimbleGen company's protocols.
Scan protocol The labeling, hybridization, and scanning following NimbleGen company's protocols.
Description PU4_T2_R1
Data processing Raw data: ORF/gene-level .calls files.
Statistical analysis was done with JMP Genomics 4.0 software (SAS Institute, Cary, NC). The data were subsequently normalized using the standard normalization algorithm (Loess) within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the FDR testing method (p < 0.05).
 
Submission date Jan 28, 2011
Last update date May 08, 2014
Contact name Shihui YANG
E-mail(s) Shihui.Yang@nrel.gov
Phone 3033847825
Organization name National Renewable Energy Lab
Department National Bioenergy Center
Street address 1617 Cole Blvd
City Golden
State/province CO
ZIP/Postal code 80401
Country USA
 
Platform ID GPL11186
Series (1)
GSE26926 Transcriptomic profile of Clostridium thermocellum ATCC27405 using switchgrass as carbon source

Data table header descriptions
ID_REF
VALUE Averaged log2 transformed normalized intensity

Data table
ID_REF VALUE
1 11.84329
2 11.74067
3 11.73009
4 12.1994
5 12.01808
6 12.07224
7 10.91172
8 11.07535
9 11.0203
10 10.26544
11 10.20519
12 10.09174
13 10.67445
14 10.68312
15 10.55156
16 9.669011
17 9.614642
18 9.575606
19 10.56882
20 10.67979

Total number of rows: 9195

Table truncated, full table size 123 Kbytes.




Supplementary file Size Download File type/resource
GSM662993.txt.gz 96.5 Kb (ftp)(http) TXT
Processed data included within Sample table

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