|
| Status |
Public on Nov 21, 2014 |
| Title |
Digits 4C Hoxa13 |
| Sample type |
SRA |
| |
|
| Source name |
4C E12.5 mouse digits
|
| Organism |
Mus musculus |
| Characteristics |
age: E12.5
tissue: Forelimb digits
viewpoint: Hoxa13
|
| Treatment protocol |
4C–seq libraries were constructed as described before (Noordermeer et al. 2011, Science).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue were made single cell by collagenase treatment. Chromatin was crosslinked in the presence of 2% formaldehyde. Cross-linked chromatin was digested with NlaIII, ligated, cross links were reversed and DNA was further digested by DpnII and again ligated under diluted conditions.
PCR amplification using primers with included adapter sequences (for Illumina HiSeq) as described before (Noordermeer et al. 2011, Science).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
library strategy: 4C
|
| Data processing |
De-multiplexing, mapping and 4C-seq were done through HTSstation (David et al, 2014 and http://htsstation.epfl.ch/).
Mapped reads were translated to restriction fragments using the HTSstation (David et al, 2014 and http://htsstation.epfl.ch/).
4C figures were made using a running mean algorithm with a window size of eleven fragments.
4C-seq was performed as previously described (Noordermeer et al. 2011)
Genome_build: mm9
Supplementary_files_format_and_content: Signal/restriction fragment or smoothed (bedGraph) for each viewpoint
|
| |
|
| Submission date |
Oct 10, 2014 |
| Last update date |
May 15, 2019 |
| 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 |
GPL17021 |
| Series (2) |
| GSE62265 |
Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci (4C-seq) |
| GSE62269 |
Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci |
|
| Relations |
| Reanalyzed by |
GSE123131 |
| BioSample |
SAMN03104580 |
| SRA |
SRX731075 |
