NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM502583 Query DataSets for GSM502583
Status Public on Dec 31, 2010
Title Jejunum_normal_rep3
Sample type RNA
 
Source name Jejunum_normal
Organism Canis lupus familiaris
Characteristics tissue: Jejunum
disease: normal
Extracted molecule total RNA
Extraction protocol RNA was extracted from all samples using TRIzol according to manufacturer's instructions (Invitrogen, Carlsbad, CA). Samples were then further purified using Qiagen miniprep RNA clean up (Qiagen, Valencia, CA) as per Affymetrix protocols for array preparation. Samples were quantified and assessed for quality using a Bioanalyzer 2100 instrument (Agilent Technologies, Palo Alto, CA).
Label biotin
Label protocol Five micrograms of purified RNA was reverse transcribed and used to make biotinylated cRNA according to standard Affymetrix protocol.
 
Hybridization protocol Samples were hybridized to Canine Genome Version 2.0 Affymetrix oligonucleotide arrays according to manufacturer's instructions (Affymetrix, Santa Clara, CA) at the NCI Microarray Core Facility (Frederick, MD).
Scan protocol Samples were scanned using an Affymetrix GeneChip scanner 3000. Data were collected using Affymetrix GCOS software.
Description Jejunum3
Data processing Affymetrix .CEL files containing the raw, probe-level signal intensities were analyzed using PartekĀ® software, version 6.4 (build 6.09.0310, Copyright 1993-2009, Partek Inc. Partek and all other Partek Inc. product or service names are registered trademarks or trademarks of Partek Inc., St. Louis, MO, USA.). Robust multichip averaging (RMA) was used for pre-processing of probe-level data (using only interrogating probes) including pre-background adjustment for GC content and probe sequence followed by RMA background correction. All chips underwent quantile normalization and probeset summaries were median polished (Bolstad, Irizarry, Astrand and Speed 2003).
 
Submission date Jan 29, 2010
Last update date Dec 31, 2010
Contact name Joseph Briggs
E-mail(s) briggsjw@gmail.com
Organization name National Cancer Institute
Department Pediatric Oncology Branch
Lab Tumor Metastasis Biology Section
Street address 37 Convent Drive
City Gaithersburg
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL3738
Series (1)
GSE20113 Canine normal tissue gene expression profiles

Data table header descriptions
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
Cfa.100.1.S1_at 9.32015
Cfa.100.1.S1_s_at 7.67569
Cfa.100.1.S2_at 4.78098
Cfa.10001.1.A1_at 3.71974
Cfa.10002.1.A1_at 4.5441
Cfa.10004.1.A1_at 3.99888
Cfa.10005.1.A1_at 3.221
Cfa.10006.1.A1_at 4.26105
Cfa.10007.1.A1_s_at 8.25688
Cfa.10008.1.A1_at 3.60828
Cfa.10009.1.A1_at 4.45994
Cfa.10010.1.A1_at 3.45908
Cfa.10011.1.A1_at 3.33187
Cfa.10012.1.A1_at 8.21879
Cfa.10013.1.A1_at 8.67407
Cfa.10014.1.A1_at 3.65795
Cfa.10015.1.A1_at 5.58062
Cfa.10016.1.A1_at 7.35483
Cfa.10017.1.A1_at 4.08372
Cfa.10018.1.A1_s_at 3.78565

Total number of rows: 42860

Table truncated, full table size 1183 Kbytes.




Supplementary file Size Download File type/resource
GSM502583.CEL.gz 3.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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