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Sample GSM1415462 Query DataSets for GSM1415462
Status Public on Jun 19, 2014
Title All live sorted spinal cord cells, age E13.5 biological rep. 1
Sample type RNA
 
Source name Aldh1L1-GFP flow sorted spinal cord
Organism Mus musculus
Characteristics genetic background: Swiss-Webster
age: E13.5
cell type: whole spinal cord
Treatment protocol papain dissociated and flow sorted on a BD facs aria II to isolate astrocytes (aldh1l1-GFP positive) and non-astrocytes (Aldh1l1-GFP negative),
Growth protocol mouse spinal cords from Aldh1l1-GFP transgenic mice on a swiss-webster background, various ages
Extracted molecule total RNA
Extraction protocol RNA was trizol purified with glycogen as a carrier molecule, DNAse digested, and further purified on an RNAeasy mini column (Qiagen)
Label biotin
Label protocol purified RNA was amplified and biotin labeled (WT ovation, NuGen)
 
Hybridization protocol standard Affymetrix protocol
Scan protocol standard Affymetrix protocol
Data processing data preprocessed in R using Bioconductor suite- oligo package/RMA algorithm used to background correct, normalize, and summarize. Two types of analyses then performed: 1) Limma package/treat algorithm used to assess differential expression, 2) Gene coexpression modules determined as described in Molofsky et al, Glia (2013) 61:1518
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.na30.mm9.probeset.csv
 
Submission date Jun 18, 2014
Last update date Jun 19, 2014
Contact name David Rowitch
Organization name University of California-San Francisco
Department Institute for Regenerative Medicine
Lab Rowitch
Street address 35 Medical Center Way, RMB 932D
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platform ID GPL6246
Series (1)
GSE58614 Expression profiling of Aldh1l1-precursors in the developing spinal cord reveals glial lineage-specific genes and direct Sox9-Nfe2l1 interactions

Data table header descriptions
ID_REF
VALUE RMA signal estimates from Oligo Bioconductor software version 2.4

Data table
ID_REF VALUE
10338001 13.19935882
10338002 7.071261701
10338003 11.57930792
10338004 10.73968418
10338005 3.057012878
10338006 3.369036521
10338007 3.830461466
10338008 4.798007011
10338009 7.739908477
10338010 3.073258245
10338011 6.665814965
10338012 3.1589824
10338013 2.91312863
10338014 2.989214104
10338015 2.970347508
10338016 7.600366015
10338017 13.55895664
10338018 7.353055911
10338019 6.226160679
10338020 7.850082047

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM1415462_04.E13W-A.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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