|
| Status |
Public on Mar 12, 2014 |
| Title |
Control mouse |
| Sample type |
RNA |
| |
|
| Source name |
Bone marrow stromal nestin+ cells, control
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: Nes-gfp
cell type: bone marrow CD45- CD31- Ter119- Nes-GFP+ cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was obtained using Picopure RNA isolation kit (Arcturus).
|
| Label |
Biotin
|
| Label protocol |
cDNA target was synthesized, fragmented, biotin-labeled using WT target labeling and Control Reagents (Affymetrix, vat. num. 900652), according to the procedure described in the GeneChip Whole Transcript Sense Target labeling Assay Manual, Version 4 (Affymetrix, Santa Clara, USA). cDNA was fragmented and the resulting fragments of approximately 40-70 nucleoides were monitored with Bioanalyzer using the RNA nano 6000 Chip.
|
| |
|
| Hybridization protocol |
The hybridisation cocktail containing fragmented biotin-labeled target DNA was transferred into Affymetrix GeneChip Mouse Gene 1.0 ST Arrays and incubated at 45 degrees on a rotator in a hybridisation oven 640 (Affymetrix) for 17 hours at 60rpm. The arrays were washed and stained on a Fluidics Station 450 by using Hybridisation Wash and Stain Kit (Affymetrix, cat. nu. 900720) using fluidics procedure FS450_0007.
|
| Scan protocol |
The GeneChips were processed with an Affymetrix GeneChip Scanner 3000 7G. DAT image files of the microarrays were generated using Affymetrix GeneChip Command Console (AGCC, version 0.0.0.676).
|
| Description |
Control
Gene expression profiling of bone marrow stromal nestin+ cells isolated 10 weeks after transplantation with control bone marrow cells.
|
| Data processing |
Data normalisation was performed using the Robust Multi-array Average (RMA) algorithm. To perform principal component analysis (PCA) comparison with previously published data, GEO data sets were downloaded and pre-processed using the GEOquery Bioconductor package. Normalised data sets were adjusted to the same intensity range, and batch effect correction was performed using ComBat.
|
| |
|
| Submission date |
Mar 11, 2014 |
| Last update date |
Mar 26, 2014 |
| Contact name |
Simón Méndez-Ferrer |
| E-mail(s) |
smendez@cnic.es
|
| Organization name |
CNIC
|
| Lab |
Stem cell niche pathophysiology
|
| Street address |
Calle Melchor Fernández Almagro, 3
|
| City |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL6246 |
| Series (2) |
| GSE55801 |
Sympathetic neuropathy of the bone marrow haematopoietic stem cell niche is essential for myeloproliferative neoplasms |
| GSE55802 |
Neuropathy of haematopoietic stem cell niche is essential for myeloproliferative neoplasms |
|
