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Sample GSM636706 Query DataSets for GSM636706
Status Public on Sep 13, 2011
Title MIY_day_3-4
Sample type RNA
 
Source name Dot1l flox/flox day 3 after transduction with control
Organism Mus musculus
Characteristics strain: B6129
cell type: MLL-AF9 leukemia cells
genotype: Dot1l flox/flox
days after transduction: 3
Treatment protocol Sorted GFP-positive Dot1l flox/flox MLL-AF9 leukemia cells were transduced with retroviral Cre-YFP or YFP control vector. GFP/YFP positive cells were sorted on days 3, 5, and 7.
Growth protocol Leukemias were generated by injecting 100 000 MLL-AF9-GFP transduced Dot1l flox/flox 4 days after transduction into B6129 recipients. Bulk leukemia cells were isolated from leukemic mice.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol. RNA was prepared using the Nugen Ovation Pico WTA system.
Label Biotin
Label protocol Amplified cDNA was labeled using the Nugene Encore TM Biotin Module.
 
Hybridization protocol 5 μg of labeled cDNA was hybridized to the Affymetrix 430 2.0 microarray using standard conditions.
Scan protocol GeneChip Scanner 3000, 7G. Standard Affymetrix protocol.
Description Loss of Dot1l in MLL-AF9 murine leukemia.
Data processing RMA background correction and quantile normalization was done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/), which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al. Biostatistics (2003).
 
Submission date Dec 07, 2010
Last update date Sep 13, 2011
Contact name Amit Sinha
E-mail(s) amit.sinha@childrens.harvard.edu
Phone 617-582-7579
Organization name Dana-Farber Cancer Institute
Department Pediatric Oncology
Lab Armstrong Lab
Street address 44 Binney St
City Boston
State/province MA
ZIP/Postal code 02135
Country USA
 
Platform ID GPL1261
Series (1)
GSE25911 Expression changes after loss of Dot1l in murine MLL-AF9 leukemia cells

Data table header descriptions
ID_REF
VALUE RMA-normalized intensity

Data table
ID_REF VALUE
1415670_at 4348.185161
1415671_at 3136.628752
1415672_at 2346.483486
1415673_at 1191.331749
1415674_a_at 918.5437129
1415675_at 437.462454
1415676_a_at 2224.876439
1415677_at 1468.646573
1415678_at 1699.917119
1415679_at 1630.968706
1415680_at 1074.584253
1415681_at 939.2552216
1415682_at 901.1547843
1415683_at 2188.191789
1415684_at 175.9227608
1415685_at 743.9033888
1415686_at 2783.26
1415687_a_at 2764.204111
1415688_at 515.6373325
1415689_s_at 429.5217343

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM636706.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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