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Sample GSM1415464 Query DataSets for GSM1415464
Status Public on Jun 19, 2014
Title All live sorted spinal cord cells, age E13.5 biological rep. 3
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
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
VALUE RMA signal estimates from Oligo Bioconductor software version 2.4

Data table
10338001 13.07220927
10338002 7.121021571
10338003 11.42655634
10338004 10.55865369
10338005 3.039383595
10338006 3.323518484
10338007 3.800309791
10338008 4.817063412
10338009 7.83257232
10338010 3.045047113
10338011 6.681259345
10338012 3.137698666
10338013 2.865492203
10338014 2.943501581
10338015 2.922265291
10338016 7.638066723
10338017 13.39597906
10338018 7.42088751
10338019 6.24478099
10338020 8.009568318

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.

Supplementary file Size Download File type/resource
GSM1415464_06.E13W-C.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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