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Sample GSM728677 Query DataSets for GSM728677
Status Public on May 21, 2011
Title LSK BL6 WT rep1
Sample type RNA
 
Source name Sorted LSK cells from WT animals
Organism Mus musculus
Characteristics marker phenotype: CD3e-,CD4-,CD5-,CD8a-,CD19-,CD45R/B220-,CD11b-,Gr1-,Ter119-,Sca1+,ckit+
marker phenotype short name: LSK
genotype: Msi2+/+
cell type: LSK
genetic background: C57/Bl6
Growth protocol BM cells were pooled from 4 Msi2Gt/Gt females (aged 6-7 weeks) or 4 C57/Bl6 females (aged 6-7 weeks) and subjected to lineage depletion. Cells from each pool were stained with fluorochrome-labelled anti-c-Kit and anti-Sca-1 monoclonal antibodies to mark LSK cells (defined as Lineage- Sca-1+ c-kit+) and Kit+ (defined as Lineage-, Sca-1-, c-kit+) and sorted by FACS into PBS+5%FBS.
Extracted molecule total RNA
Extraction protocol Cells were pelleted and RNA was extracted using the RNeasy Mini Kit (Qiagen) by the manufacturer's instructions.
Label Cy3
Label protocol cDNA from 25 ng of RNA was transcribed with T7 RNA polymerase in the presence of Cy3-CTP to produce labelled cRNA using the standard Agilent labelling protocol.
 
Hybridization protocol The labelled cRNA was hybridized to the Agilent Whole Mouse Genome 4x44k 60-mer oligo microarray using stnadard Agilent protocol.
Scan protocol The arrays were scanned on an Agilent G2565CA microarray scanner at 110% PMT and 5 μm resolution.
Data processing Intensity data was extracted using the Feature Extraction v 10.7.3.1 software (Agilent) and corrected for background noise using the normexp method [Ritchie ME etal. 2007. Bioinformatics]. To assure comparability across samples we use quantile normalization [Bolstad, B. (2001). Unpublished manuscript http://bmbolstad.com/stuff/qnorm.pdf].
 
Submission date May 20, 2011
Last update date May 21, 2011
Contact name Eric M. Kallin
E-mail(s) eric.kallin@crg.es
Organization name Center for Genomic Regulation
Department Differentiation and Cancer
Lab Thomas Graf
Street address C/ Dr. Aiguader, 88
City Barcelona
State/province Barcelona
ZIP/Postal code 08003
Country Spain
 
Platform ID GPL10333
Series (1)
GSE29432 Musashi 2 is a regulator of the hematopoietic stem cell compartment identified by a retroviral insertion screen and knockout mice

Data table header descriptions
ID_REF
VALUE Log2 normalized probe intensity

Data table
ID_REF VALUE
16881 11.72
4277 12.33
14192 12.70
19677 12.69
22939 12.66
23005 12.71
33417 12.64
37653 12.40
41272 12.41
41962 12.38
42438 12.47
4751 6.05
27573 11.21
547 8.22
11423 8.49
14917 8.44
16964 8.46
26657 8.45
26991 8.45
33432 8.46

Total number of rows: 43020

Table truncated, full table size 464 Kbytes.




Supplementary file Size Download File type/resource
GSM728677_01_MA_1100252665510163_Cy3_BL6_Y_LSK_1_1_1.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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