|
| Status |
Public on Mar 03, 2017 |
| Title |
control4 |
| Sample type |
RNA |
| |
|
| Source name |
Freshly isolated Atg12flox/flox HSCs
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: bone marrow
cell type: hematopoietic stem cell
genotype: atg12f/f
age: 3-4 months
cell markers: Lin-/c-Kit+/Sca-1+/Flk2-/CD150+/CD48-
|
| Growth protocol |
freshly double sorted HSCs from mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Arcturus PicoPure RNA Isolation Kit, amplified using Ovation Pico WTA System V2
|
| Label |
biotin
|
| Label protocol |
Sense-strand complementary DNA targets were generated using the NuGEN WT-Ovation Exon Module, fragmented and biotinylated using the Encore Biotin Module.
|
| |
|
| Hybridization protocol |
Hybridized on Affymetrix Gene ST 1.0 microarrays according to manufacturers’ instructions.
|
| Scan protocol |
The signal intensity fluorescent images produced during the Affymetrix GeneChip hybirdizations were read using the Affymetrix Model 3000 Scanner and converted into GeneChip probe results files (CEL) using Command and Expression Console software (Affymetrix).
|
| Description |
Gene expression data from freshly isolated Atg12flox/flox HSCs
|
| Data processing |
Gene expression was first measured at the probe set level (n = 241,619) using the RMA (Robust Multi-array Average) methodology followed by quantile normalization. Quality of the data was assessed using principal component analysis (PCA) as well as unsupervised hierarchical clustering. Probe set annotation for the MoGene1.0st v1 array was downloaded from Affymetrix's website and the 241,619 probe sets were mapped to the 28,853 main transcript set (excluding controls). This data set was used for all analyses. We used a family of generalized, linear models implemented with the R package, LIMMA, to assess differential expression between groups of interest.
|
| |
|
| Submission date |
May 21, 2016 |
| Last update date |
Mar 03, 2017 |
| Contact name |
Emmanuelle Passegue |
| E-mail(s) |
passeguee@stemcell.ucsf.edu
|
| Phone |
415-476-2426
|
| Organization name |
The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California San Francisco
|
| Department |
Department of Medicine, Hem/Onc Division
|
| Street address |
35 Medical Center Way, RMB-1017, Box 0667
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (2) |
| GSE81719 |
Autophagy maintains metabolism and functional activity of a subset of aged hematopoietic stem cells [gene expression] |
| GSE81721 |
Autophagy maintains metabolism and functional activity of a subset of aged hematopoietic stem cells |
|
