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Sample GSM502598 Query DataSets for GSM502598
Status Public on Dec 31, 2010
Title LymphNode_normal_rep2
Sample type RNA
 
Source name LymphNode_normal
Organism Canis lupus familiaris
Characteristics tissue: Lymph Node
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 LymphNode2
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 10.0601
Cfa.100.1.S1_s_at 7.63201
Cfa.100.1.S2_at 5.89456
Cfa.10001.1.A1_at 3.46823
Cfa.10002.1.A1_at 8.19138
Cfa.10004.1.A1_at 3.68399
Cfa.10005.1.A1_at 3.38818
Cfa.10006.1.A1_at 4.2772
Cfa.10007.1.A1_s_at 6.98499
Cfa.10008.1.A1_at 3.47028
Cfa.10009.1.A1_at 6.2054
Cfa.10010.1.A1_at 3.35116
Cfa.10011.1.A1_at 3.46775
Cfa.10012.1.A1_at 8.58607
Cfa.10013.1.A1_at 8.43523
Cfa.10014.1.A1_at 3.89157
Cfa.10015.1.A1_at 5.60909
Cfa.10016.1.A1_at 5.37839
Cfa.10017.1.A1_at 3.36025
Cfa.10018.1.A1_s_at 3.69882

Total number of rows: 42860

Table truncated, full table size 1183 Kbytes.




Supplementary file Size Download File type/resource
GSM502598.CEL.gz 3.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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