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Sample GSM841639 Query DataSets for GSM841639
Status Public on Dec 15, 2011
Title Lithium_rep3
Sample type RNA
 
Source name 7-day cultured HSPCs with Lithum
Organism Mus musculus
Characteristics strain: C57Bl/6
tissue: Bone Marrow HSPC
Growth protocol Freshly isolated hematopoietic stem/progenitor cells, defined by L-S+K+ phenotype, were differentiated in a liquid medium supplemented with fetal calf serum, murine stem cell factor and recombinant murine granulocyte/macrophage-colony stimulating factor. The cells were cultured for 7 days with or without 1mM VPA or 5mM LiCl or the combination. At day 7 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
Data processing Quantile normalization was applied on log2-transformed data.
Normalized matrix: GeneSpring GX 11.0-computed normalized signal intensity on log2-transformed data. Non-normalized matrix: GenomeStudio-computed raw signal intensity.
 
Submission date Dec 01, 2011
Last update date Dec 15, 2011
Contact name Leonid Bystrykh
E-mail(s) l.bystrykh@umcg.nl
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 (2)
GSE34088 The combination of valproic acid and lithium prevents hematopoietic stem/progenitor cell differentiation.
GSE35291 Expression profiles of 7-day cultured HSPCs in the presence or absence of valproic acid and/or lithium

Data table header descriptions
ID_REF
VALUE log2 quantile normalized signal intensity
Pvalue
Calls

Data table
ID_REF VALUE Pvalue Calls
ILMN_1212607 6.9626775 0.89474 P
ILMN_1212612 6.6422477 0.19549 A
ILMN_1212619 6.761908 0.5802 A
ILMN_1212628 6.7168036 0.42982 A
ILMN_1212632 6.7043133 0.37594 A
ILMN_1212636 11.345286 1 P
ILMN_1212637 9.674209 1 P
ILMN_1212645 10.246875 1 P
ILMN_1212648 8.38279 1 P
ILMN_1212653 6.826449 0.7381 M
ILMN_1212672 8.223256 1 P
ILMN_1212682 8.116991 1 P
ILMN_1212683 6.607652 0.12657 A
ILMN_1212685 6.681805 0.32206 A
ILMN_1212692 9.65053 1 P
ILMN_1212693 6.98343 0.91103 P
ILMN_1212695 9.966946 1 P
ILMN_1212698 6.592792 0.09524 A
ILMN_1212702 7.7057624 1 P
ILMN_1212703 7.1870747 0.98872 P

Total number of rows: 25697

Table truncated, full table size 764 Kbytes.




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

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