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Sample GSM1227387 Query DataSets for GSM1227387
Status Public on Nov 04, 2013
Title TA+BA/F3_mifepriston_16h_TA_ChIP_rep2
Sample type genomic
 
Channel 1
Source name TEL-AML1 Inducible BA/F3 cell line, mifepriston, 16h
Organism Mus musculus
Characteristics genotype: hsa ETV6-RUNX1 +
sample type: immuoprecipitated DNA
cell line: BA/F3
chip antibody: TEL-AML1
Treatment protocol 32.5 pM mifepristone, 16h, TEL-AML1 ChIP
Extracted molecule genomic DNA
Extraction protocol ChIPs were performed as described by Lee, T. I., et al. (Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc 1, 729-748, doi:101284307 (2006)). 5 µg TEL-AML1 antibody for inducible cell lines or rat isotype control IgG fro controls (Abcam) were incubated with protein G magnetic beads (Dynal) pre-blocked with pre-immunization serum for 6 hours at 4°C. Beads were washed and incubated with DNA of 10 million cells sheared to ~ 500 bp length at 4°C over night. Chromatin-immunoprecipitated DNA was amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma-Aldrich Chemie GmbH)
Label Cy5
Label protocol 1 µg DNA was directly labeled by Klenow random priming with Cy5 nonamers (DNA precipitated with ETV6-RUNX1 antibody) or with Cy3 nonamers (DNA isolated from input material) per manufacturer's protocol (http://www.nimblegen.com/support/dna-microarray-support.html).
 
Channel 2
Source name TEL-AML1 Inducible BA/F3 cell line, mifepriston, 16h
Organism Mus musculus
Characteristics genotype: hsa ETV6-RUNX1 +
cell line: BA/F3
chip antibody: input
Treatment protocol 32.5 pM mifepristone, 16h
Extracted molecule genomic DNA
Extraction protocol ChIPs were performed as described by Lee, T. I., et al. (Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc 1, 729-748, doi:101284307 (2006)). 5 µg TEL-AML1 antibody for inducible cell lines or rat isotype control IgG fro controls (Abcam) were incubated with protein G magnetic beads (Dynal) pre-blocked with pre-immunization serum for 6 hours at 4°C. Beads were washed and incubated with DNA of 10 million cells sheared to ~ 500 bp length at 4°C over night. Chromatin-immunoprecipitated DNA was amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma-Aldrich Chemie GmbH)
Label Cy3
Label protocol 1 µg DNA was directly labeled by Klenow random priming with Cy5 nonamers (DNA precipitated with ETV6-RUNX1 antibody) or with Cy3 nonamers (DNA isolated from input material) per manufacturer's protocol (http://www.nimblegen.com/support/dna-microarray-support.html).
 
 
Hybridization protocol Hybridization was performed according to standard procedures by Roche Nimblegen
Scan protocol Scanning was performed according to standard procedures by Roche Nimblegen.
Data processing Log2 ratios, scaled using the Tukey biweight.
 
Submission date Sep 10, 2013
Last update date Nov 05, 2013
Contact name Pablo Landgraf
E-mail(s) pablo.landgraf@gmx.de
Organization name Heinrich-Heine University Düsseldorf
Department Clinic of Pediatric Oncology, Hematology and Clinical Immunology
Street address Moorenstraße 5
City Düsseldorf
ZIP/Postal code 40225
Country Germany
 
Platform ID GPL8943
Series (2)
GSE50730 TEL-AML1 (ETV6-RUNX1) in B-cells and leukemia (part 1)
GSE50736 TEL-AML1 (ETV6-RUNX1) in B-cells and leukemia

Data table header descriptions
ID_REF
VALUE promoter region scaled log2 ratio's (ETV6-RUNX1 IP/input material)

Data table
ID_REF VALUE
CHR10FS003132303 -0.19
CHR10FS003132403 0.04
CHR10FS003132503 -0.60
CHR10FS003132603 -0.76
CHR10FS003132703 -0.37
CHR10FS003132803 1.09
CHR10FS003132903 -0.02
CHR10FS003133003 0.55
CHR10FS003133103 1.64
CHR10FS003133303 -0.30
CHR10FS003133403 1.96
CHR10FS003133503 1.09
CHR10FS003133603 2.54
CHR10FS003133703 2.99
CHR10FS003133803 -0.12
CHR10FS003133903 -0.08
CHR10FS003134003 -0.43
CHR10FS003134103 -0.14
CHR10FS003134203 -0.04
CHR10FS003134303 -0.47

Total number of rows: 380409

Table truncated, full table size 8137 Kbytes.




Supplementary file Size Download File type/resource
GSM1227387_3068903_532.pair.gz 6.9 Mb (ftp)(http) PAIR
GSM1227387_3068903_635.pair.gz 6.9 Mb (ftp)(http) PAIR
Processed data included within Sample table

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