NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1260643 Query DataSets for GSM1260643
Status Public on May 01, 2014
Title Wild-type liver DSS colitis 7 days rep 3
Sample type RNA
 
Source name Wild-type liver DSS colitis 7 days
Organism Mus musculus
Characteristics strain background: C57BL/6
gender: female
age: 6 weeks
genotype/variation: wild-type
treated with: 3% dextran sulfate sodium (DSS) in the drinking water for 7 days
tissue: liver
Treatment protocol The mice were given 3% DSS in their drinking water for 7 days to induce colitis.
Growth protocol Mice were maintained under specific pathogen-free conditions.
Extracted molecule total RNA
Extraction protocol Mice were euthanized on completion of 7 days of DSS treatment. At necropsy, segments of liver were excised and homogenized in Trizol reagent. Total RNA was prepared according to the manufacturer's guidelines.
Label Biotin
Label protocol Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 0.1 micrograms of total RNA using amplification kit (Ambion WT Expression Kit, Lot #1210014), followed by labeling 5.5 micrograms of cDNA using Affymetrix WT Terminal Labelin Kit (Lot #4182035).
 
Hybridization protocol Following fragmentation, 5.5 micrograms of cDNA were hybridized for 16 hours at 45 degrees C on GeneChip Mouse 2.0 ST Array in an Affymetrix GeneChip hybridization oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G running Affymetrix Gene Command Console ver 3.2.
Description WT DSS c
Data processing The data was normalized by robust multichip analysis (RMA) using the Bioconductor package (v.2.12) in R (v.3.0.1).
 
Submission date Nov 07, 2013
Last update date May 01, 2014
Contact name Bobby Cherayil
E-mail(s) bcherayil@partners.org
Phone 617-726-4170
Organization name Massachusetts General Hospital
Department Pediatrics
Lab Mucosal Immunology and Biology Research Center
Street address Building 114, 16th Street
City Charlestown
State/province Massachusetts
ZIP/Postal code 02129
Country USA
 
Platform ID GPL16570
Series (1)
GSE52168 Liver transcriptional profile of wild-type and IL-10 knockout mice with colitis

Data table header descriptions
ID_REF
VALUE log-2 RMA signal

Data table
ID_REF VALUE
17200001 5.692280753
17200003 6.92059594
17200005 4.629486448
17200007 4.943211286
17200009 5.973308882
17200011 5.618446644
17200013 5.653440985
17200015 5.535384558
17200017 3.7721613
17200019 5.000895468
17200021 5.16447446
17200023 7.456843004
17200025 6.330133918
17200027 5.382792498
17200029 3.756820137
17200031 4.085124238
17200033 3.582894138
17200035 4.084477672
17200037 6.594879157
17200039 4.376613976

Total number of rows: 41345

Table truncated, full table size 843 Kbytes.




Supplementary file Size Download File type/resource
GSM1260643_WT_DSS_c_1898G.CEL.gz 9.2 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap