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Sample GSM1346229 Query DataSets for GSM1346229
Status Public on Mar 12, 2014
Title MPN mouse 1
Sample type RNA
Source name Bone marrow stromal nestin+ cells, Mx1-cre;JAK2-V617F
Organism Mus musculus
Characteristics strain/background: C57BL/6
genotype/variation: Nes-gfp;Mx1-cre;JAK2-V617F
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 01_MxCre-JAK2V617F
Gene expression profiling of bone marrow stromal nestin+ cells isolated 10 weeks after transplantation with Mx1-cre;JAK2-617F 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 12.00744
10338002 6.01183
10338003 10.51466
10338004 9.94326
10338005 2.27871
10338006 2.48932
10338007 2.79027
10338008 3.62411
10338009 7.24679
10338010 2.31682
10338011 5.63342
10338012 2.37472
10338013 2.16654
10338014 2.21131
10338015 2.19628
10338016 7.03885
10338017 12.85606
10338018 6.6056
10338019 4.94671
10338020 7.49109

Total number of rows: 35556

Table truncated, full table size 587 Kbytes.

Supplementary file Size Download File type/resource
GSM1346229_01_MxCre-JAK2V617F_MoGene-1_0-st-v1_.CEL.gz 3.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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