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Sample GSM1346232 Query DataSets for GSM1346232
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
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
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

Data table header descriptions
VALUE RMA signal intensity (log2)

Data table
10338001 12.14728
10338002 4.78229
10338003 10.27871
10338004 9.42478
10338005 2.18133
10338006 2.32257
10338007 2.49039
10338008 3.00403
10338009 5.5407
10338010 2.18564
10338011 4.46136
10338012 2.21431
10338013 2.11462
10338014 2.11249
10338015 2.13234
10338016 5.52287
10338017 12.81459
10338018 5.19951
10338019 3.86751
10338020 5.82233

Total number of rows: 35556

Table truncated, full table size 587 Kbytes.

Supplementary file Size Download File type/resource
GSM1346232_Control_MoGene-1_0-st-v1_.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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