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Sample GSM1006901 Query DataSets for GSM1006901
Status Public on Sep 25, 2012
Title Valproic_acid-stimulated_rep3
Sample type RNA
Source name 24h cultured LSK cells with Valproic Acid
Organism Mus musculus
Characteristics strain: C57Bl/6
tissue: Bone Marrow
cell type: hematopoietic stem/progenitor cell (HSPC)
cell phenotype: L-S+K+
agent: Valproic Acid
Growth protocol Freshly isolated hematopoietic stem/progenitor cells, defined by L-S+K+ phenotype, were stimulated for 24h in the presence or in the absence of 1mM valproic acid (VPA), in a liquid medium supplemented with fetal calf serum, murine stem cell factor and recombinant murine granulocyte/macrophage-colony stimulating factor. After 24h culture the cells were collected in RNA lysis buffer (Qiagen) for gene expression studies.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the RNeasy Mini kit (Qiagen) in accordance with the manufacturer’s protocol.
Label biotin
Label protocol Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion) according to the manufacturer’s specifications starting with 100 ng total RNA.
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description VPA-3
Data processing Non-normalized data: GenomeStudio-computed raw signal intensity.
Normalized data: GeneSpring GX 11.5-computed quantile-normalization was applied on log2-transformed data
Submission date Sep 20, 2012
Last update date Sep 25, 2012
Contact name Leonid Bystrykh
Organization name University Medical Center Groningen
Department European Research Institute for the Biology of Ageing - ERIBA
Lab Ageing Biology and Stem Cells
Street address A. Deusinglaan 1
City Groningen
State/province Groningen
ZIP/Postal code 9713 AV
Country Netherlands
Platform ID GPL6885
Series (1)
GSE41020 Sca-1 is an early-response target of histone deacetylase inhibitors and marks hematopoietic cells with enhanced function

Data table header descriptions
VALUE log2, quantile-normalized signal intensity

Data table
ID_REF VALUE VPA-3_P_Value VPA-3_Calls
ILMN_1212607 6.981134 0.90476 P
ILMN_1212612 6.4550915 0.00251 A
ILMN_1212619 6.853319 0.7594 M
ILMN_1212628 6.7653656 0.59023 A
ILMN_1212632 6.6924973 0.3797 A
ILMN_1212636 11.188817 1 P
ILMN_1212637 9.891566 1 P
ILMN_1212645 9.3140135 1 P
ILMN_1212648 8.774191 1 P
ILMN_1212653 6.921569 0.84712 P
ILMN_1212672 9.191985 1 P
ILMN_1212682 7.503058 1 P
ILMN_1212683 6.7250376 0.47744 A
ILMN_1212685 6.6202836 0.1792 A
ILMN_1212692 6.9892893 0.90727 P
ILMN_1212693 7.4594045 0.99875 P
ILMN_1212695 7.558847 1 P
ILMN_1212698 6.664533 0.29574 A
ILMN_1212702 7.3460183 0.99373 P
ILMN_1212703 7.241252 0.98872 P

Total number of rows: 25697

Table truncated, full table size 763 Kbytes.

Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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