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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).
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|
|
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.
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|
|
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 |
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