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Sample GSM896372 Query DataSets for GSM896372
Status Public on Apr 11, 2012
Title M4727-liver-Chronic, 461100_A02
Sample type RNA
 
Source name Woodchuck liver, chronic
Organism Marmota monax
Characteristics tissue: liver
whv infection status: chronic
sample identifier: M4727
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from woodchuck liver tissues using the QIAamp RNA Blood Mini Kit (Qiagen Inc., Valencia, CA).
Label Cy3
Label protocol 10 μg of total RNA was reverse-transcribed using the SuperScript double-stranded cDNA synthesis kit (Invitrogen, Inc., Calsbad, CA). After precipitation, double-stranded cDNA was labelled with Cy3 by using the Roche NimbleGen One-color DNA Labelling Kit (Roche NimbleGen, Inc., Madison, WI).
 
Hybridization protocol Woodchuck Gene Expression HX3 Microarrays were hybridized with 6.7 μg Cy3-labelled cDNA for 16-20 hours at 42ºC and were washed and dried according to the manufacturer’s instructions.
Scan protocol Microarrays were scanned using a Roche NimbleGen MS200 Microarray Scanner at 2 μm pixel resolution. Features were extracted using NimbleScan Software.
Description 461100_A02
mRNA
Data processing The gene expression data was normalized by the Robust Multichip Average (RMA) algorithm implemented in Partek Genomics Suite 6.5 (Partek, St. Louis MO).
 
Submission date Mar 15, 2012
Last update date Apr 11, 2012
Contact name Donavan Cheng
E-mail(s) donavan.cheng@gmail.com
Organization name Hoffmann-LaRoche
Department Translational Research Sciences
Street address 340 Kingsland Ave
City Nutley
State/province NJ
ZIP/Postal code 07110
Country USA
 
Platform ID GPL15354
Series (2)
GSE36250 Transcriptomic analysis of the woodchuck model of chronic hepatitis B
GSE36533 Transcriptomic analysis of the woodchuck model of chronic hepatitis B: Liver gene expression in uninfected, resolved and chronically infected woodchucks

Data table header descriptions
ID_REF
VALUE Log2 RMA value

Data table
ID_REF VALUE
Chimeric_isotig02648 9.01432
Chimeric_isotig05571 7.91045
Chimeric_isotig05812 9.30888
Chimeric_isotig06356 8.84074
Chimeric_isotig06378 9.48844
Chimeric_isotig06494 10.3321
Chimeric_isotig06667 6.67724
Chimeric_isotig06765 5.93669
Chimeric_isotig07262 8.49511
Chimeric_isotig07407 6.0743
Chimeric_isotig08256 6.59502
Chimeric_isotig08537 6.73741
Chimeric_isotig08963 6.38549
Chimeric_isotig09077 8.15886
Chimeric_isotig09205 8.83552
Chimeric_isotig09239 10.2125
Chimeric_isotig09244 9.72433
Chimeric_isotig09305 9.20415
Chimeric_isotig09306 6.584
Chimeric_isotig09439 9.46325

Total number of rows: 36184

Table truncated, full table size 1188 Kbytes.




Supplementary file Size Download File type/resource
GSM896372_461100_A02_532.pair.gz 11.7 Mb (ftp)(http) PAIR
Processed data included within Sample table

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