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Sample GSM502607 Query DataSets for GSM502607
Status Public on Dec 31, 2010
Title SkeletalMuscle_normal_rep4
Sample type RNA
 
Source name SkeletalMuscle_normal
Organism Canis lupus familiaris
Characteristics tissue: Skeletal Muscle
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 SkeletalMuscle4
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 6.82031
Cfa.100.1.S1_s_at 4.5731
Cfa.100.1.S2_at 3.45888
Cfa.10001.1.A1_at 3.84497
Cfa.10002.1.A1_at 4.08475
Cfa.10004.1.A1_at 3.98972
Cfa.10005.1.A1_at 3.47332
Cfa.10006.1.A1_at 3.78259
Cfa.10007.1.A1_s_at 7.77943
Cfa.10008.1.A1_at 3.5684
Cfa.10009.1.A1_at 4.1812
Cfa.10010.1.A1_at 3.44936
Cfa.10011.1.A1_at 3.49578
Cfa.10012.1.A1_at 8.93748
Cfa.10013.1.A1_at 6.94139
Cfa.10014.1.A1_at 4.13224
Cfa.10015.1.A1_at 6.57379
Cfa.10016.1.A1_at 8.19179
Cfa.10017.1.A1_at 3.21195
Cfa.10018.1.A1_s_at 3.755

Total number of rows: 42860

Table truncated, full table size 1183 Kbytes.




Supplementary file Size Download File type/resource
GSM502607.CEL.gz 3.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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