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Sample GSM1524256 Query DataSets for GSM1524256
Status Public on Nov 21, 2014
Title Digits 4C Hoxd13
Sample type SRA
Source name 4C E12.5 mouse digits
Organism Mus musculus
Characteristics age: E12.5
tissue: Forelimb digits
viewpoint: Hoxd13
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
Mapped reads were translated to restriction fragments using the HTSstation (David et al, 2014 and
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
Reanalyzed by GSE123131
BioSample SAMN03104578
SRA SRX731073

Supplementary file Size Download File type/resource 211.0 Kb (ftp)(http) BW
GSM1524256_segToFrag_4C_Digits_WT_E12-5_HoxD13_smoothed_11FragsPerWin.bedGraph.gz 1.1 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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