|
| Status |
Public on Nov 21, 2014 |
| Title |
Input |
| Sample type |
genomic |
| |
|
| Source name |
Input DNA from E12.5 mouse limbs
|
| Organism |
Mus musculus |
| Characteristics |
antibody: none
age: E12.5
developmental stage: Embryo
tissue: Forelimb/ autopod
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was carried out according to (Lee et al., 2006) on pool of 20 genital tubercles dissected at E15.5 or E13.5, fixed for 15 minutes in 1% formaldehyde and using 4μl of anti-H3K27me3 (Millipore, 17-622) or H3K27ac (abcam ab4729) antibodies, immunoprecipated with EZview Red protein G/A affinity Gel beads from Sigma. ChIP were amplified using ligation mediated-PCR, then fragmented, labeled and hybridized to custom tiling array (Lee et al., 2006).
|
| Label |
biotin
|
| Label protocol |
1 ug of ChIP was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
1μg of DNA was hybridzed per array for 16 hours at 45° at 60rpm using the Affymetrix hybridization kit.
|
| Scan protocol |
Arrays were scanned on an Affymetrix Scanner 3000 7G
|
| Data processing |
Data were quantile normalized within ChIP replicate groups against input and scaled to medial feature intensity of 100 using TAS software (Affymetrix). PM-MM pairs mapping within a sliding window of 250 bp was used.
bar files of normalized signals are generated by TAS software (Affymetrix).
|
| |
|
| Submission date |
Oct 06, 2014 |
| Last update date |
Nov 21, 2014 |
| Contact name |
Nicolas Lonfat |
| Organization name |
EPFL - Ecole Polytechnique Fédérale de Lausanne
|
| Department |
School of Life Sciences
|
| Lab |
Laboratory of developmental genomics
|
| Street address |
EPFL-SV-ISREC-UPDUB- Station 19
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL14183 |
| Series (2) |
| GSE62073 |
Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci (tiling) |
| GSE62269 |
Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci |
|
