|
| Status |
Public on Nov 04, 2013 |
| Title |
BA/F3_TEL_ChIP_rep3 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Ba/F3 cell line
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wt
sample type: immuoprecipitated DNA
cell line: BA/F3
chip antibody: anti-TEL (N-19; Santa Cruz Biotechnology)
|
| 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)). The mouse endogenous TEL protein was immunoprecipitated with antibody anti-TEL (N-19; Santa Cruz Biotechnology) following the suppliers instructions. 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 TEL 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 |
Ba/F3 cell line
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wt
cell line: BA/F3
chip antibody: input
|
| 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)). The mouse endogenous TEL protein was immunoprecipitated with antibody anti-TEL (N-19; Santa Cruz Biotechnology) following the suppliers instructions. 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 TEL 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) |
[email protected]
|
| 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) |
| GSE50731 |
TEL-AML1 (ETV6-RUNX1) in B-cells and leukemia (part 2) |
| GSE50736 |
TEL-AML1 (ETV6-RUNX1) in B-cells and leukemia |
|
