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Sample GSM896357 Query DataSets for GSM896357
Status Public on Apr 11, 2012
Title M4388-liver-Chronic, 461059_A01
Sample type RNA
 
Source name Woodchuck liver, chronic
Organism Marmota monax
Characteristics tissue: liver
whv infection status: chronic
sample identifier: M4388
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 461059_A01
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 8.36707
Chimeric_isotig05571 7.55405
Chimeric_isotig05812 9.68013
Chimeric_isotig06356 8.8522
Chimeric_isotig06378 9.44904
Chimeric_isotig06494 9.88617
Chimeric_isotig06667 6.80656
Chimeric_isotig06765 5.57805
Chimeric_isotig07262 8.74858
Chimeric_isotig07407 6.02003
Chimeric_isotig08256 7.36781
Chimeric_isotig08537 6.32688
Chimeric_isotig08963 6.62316
Chimeric_isotig09077 8.44004
Chimeric_isotig09205 8.55703
Chimeric_isotig09239 10.4101
Chimeric_isotig09244 9.65226
Chimeric_isotig09305 9.22209
Chimeric_isotig09306 6.4793
Chimeric_isotig09439 9.78648

Total number of rows: 36184

Table truncated, full table size 1188 Kbytes.




Supplementary file Size Download File type/resource
GSM896357_461059_A01_532.pair.gz 11.6 Mb (ftp)(http) PAIR
Processed data included within Sample table

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