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Sample GSM1149514 Query DataSets for GSM1149514
Status Public on May 28, 2013
Title SJL-ChrY^B10.S, young, macrophage, rep2
Sample type RNA
 
Source name SJL-ChrY^B10.S, thioglycollate-elicited peritoneal macrophages, naïve, young
Organism Mus musculus
Characteristics strain/background: SJL-ChrY^B10.S
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 YYA#2
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 12.7253
10338002 4.87091
10338003 11.4535
10338004 10.6861
10338005 2.65843
10338006 2.79554
10338007 2.91412
10338008 3.19567
10338009 6.43175
10338010 2.68681
10338011 4.54677
10338012 2.7266
10338013 2.57625
10338014 2.61417
10338015 2.54115
10338016 5.79379
10338017 13.0824
10338018 5.29501
10338019 3.9963
10338020 6.55062

Total number of rows: 65529

Table truncated, full table size 1081 Kbytes.




Supplementary file Size Download File type/resource
GSM1149514_YYA_2-Teuscher-3-23-2012-Pico_Ovation_Exon-8.7.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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