|
| 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
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 |
|
