|
| Status |
Public on Feb 20, 2009 |
| Title |
HSC_dKO_1 |
| Sample type |
RNA |
| |
|
| Source name |
Lin-Sca1+CD150+CD48-HSCs_dKO1
|
| Organism |
Mus musculus |
| Characteristics |
Mouse model: MxCre c-myc f2 N-myc f2 on a mixed background
Age: 8 weeks old
Tissue: Bone marrow LT-HSCs (Lin- Sca1+ CD150+ CD48-)
|
| Treatment protocol |
2 daily pI-pC treatment, last treatment 3 days prior to sacrifice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from sorted cells was purified using Trizol extraction followed by ethanol precipitation and 2 rounds of amplification with the Nugen WT-Ovation Pico RNA Amplification System.
|
| Label |
biotin
|
| Label protocol |
See Affymetrix GeneChip® Two-Cycle Target Labeling Assay protocol, Affymetrix GeneChip ® IVT labeling kit
|
| |
|
| Hybridization protocol |
Affymetrix GeneChip® Hybridization Control Kit
|
| Scan protocol |
Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software.
|
| Description |
HSC_dKO_1
|
| Data processing |
Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.
|
| |
|
| Submission date |
Aug 16, 2008 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Elisa Laurenti |
| E-mail(s) |
[email protected]
|
| Phone |
0041216925816
|
| Organization name |
EPFL
|
| Department |
ISREC
|
| Lab |
Trumpp
|
| Street address |
Chemin Des Boveresses 155
|
| City |
Epalinges |
| ZIP/Postal code |
1066 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL1261 |
| Series (2) |
| GSE12467 |
Differentially regulated genes in control and c-myc N-myc deficient LT-HSCs |
| GSE12538 |
Differentially regulated genes in control and c-myc N-myc deficient LT-HSCs and progenitors |
|
| Relations |
| Reanalyzed by |
GSE119085 |
