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Sample GSM1149509 Query DataSets for GSM1149509
Status Public on May 28, 2013
Title SJL, young, macrophage, rep3
Sample type RNA
 
Source name SJL, thioglycollate-elicited peritoneal macrophages, naïve, young
Organism Mus musculus
Characteristics strain/background: SJL
gender: male
age: ≤ 4 weeks
cell type: thioglycollate-elicited peritoneal macrophages
cell purification: adherent cells
Extracted molecule total RNA
Extraction protocol RNA was isolated from live cells using the Qiagen RNeasy® Plus Mini Kit following the manufacturer's instructions (Qiagen, Valencia, CA).
Label Biotin
Label protocol Oligonucleotide microarray analysis of RNA expression levels was performed in the Vermont Genetics Network Microarray Facility using the Affymetrix GeneChip Platform (Affymetrix Inc., Santa Clara, CA) according to manufacturer's protocols. In brief, the Nugen Ovation system v.2 with SPIA® RNA amplification was employed to convert 50ng of total RNA to cDNA. This isothermal RNA amplification system produces 5-12 ug of anti-sense cDNA targets that is followed by several steps to produce sense strand cDNA to be fragmented, biotinylated and hybridized to the GeneChip.
 
Hybridization protocol After purification and fragmentation, biotinylated-cDNA targets were hybridized to the Mouse Gene 1.0 ST Arrays oligonucleotide arrays for 16 hours at 45oC. Hybridized arrays were washed and stained with streptavidin-phycoerythrin followed by sequential incubations with biotin-coupled polyclonal anti-streptavidin antibody and streptavidin phycoerythrin as a fluorescent amplification step.
Scan protocol After staining, arrays were scanned (3000-7G Scanner, Affymetrix Inc., Santa Clara, CA) and data collected for statistical analysis.
Description SYA#3
Data processing Raw GeneChip data (one DAT file for each chip) includes a collection of images, one for each probe and chip. Each image was summarized by Affymetrix GCOS software using one probe intensity (in CEL files, one per chip).sample.
Information from multiple probes was combined to obtain a single measure of expression for each probe set and sample. Probe-level intensities were calculated using the Robust Multichip Average (RMA) algorithm, including background-correction, normalization (quantile), and summarization (median polish), for each probe set and sample, as is implemented in Partek Genomic Suites®, version 6.6 (Copyright © 2009, Partek Inc., St. Louis, MO, USA).
probe group file: MoGene-1_0-st-v1.r4.pgf
meta-probeset file: MoGene-1_0-st-v1.na32.mm9.transcript.csv
 
Submission date May 28, 2013
Last update date May 28, 2013
Contact name Laure Case
E-mail(s) lcase@uvm.edu
Organization name University of Vermont
Street address 89 Beaumont Ave
City Burlington
ZIP/Postal code 05405
Country USA
 
Platform ID GPL10740
Series (2)
GSE47437 Lymph node CD4+ T cell and thioglycollate-elicited peritoneal macrophage expression data from naïve young and old SJL/J and SJL-ChrY^B10.S male mice
GSE47440 The Y chromosome as a regulatory element shaping immune cell transcriptomes and susceptibility to autoimmune disease

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
10338001 11.9239
10338002 4.31408
10338003 9.87563
10338004 9.04105
10338005 2.1612
10338006 2.29519
10338007 2.47104
10338008 2.79914
10338009 4.83518
10338010 2.16996
10338011 3.95047
10338012 2.20083
10338013 2.03887
10338014 2.10033
10338015 2.05584
10338016 4.89395
10338017 12.6924
10338018 4.63384
10338019 3.59001
10338020 5.20881

Total number of rows: 65529

Table truncated, full table size 1080 Kbytes.




Supplementary file Size Download File type/resource
GSM1149509_SYA_3-Teuscher-3-23-2012-Pico_Ovation_Exon-9.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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