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Sample GSM2713719 Query DataSets for GSM2713719
Status Public on Dec 22, 2017
Title PL_HiC_E12_del1-13d9lac
Sample type SRA
 
Source name Proximal forelimbs and proximal hindlimbs
Organism Mus musculus
Characteristics tissue: Proximal forelimbs and proximal hindlimbs
genotype: delHoxd(1-13)d9lac
strain: B6CBAF4
embryonic day: E12.5
Extracted molecule genomic DNA
Extraction protocol Hi-C libraries were generated using the HindIII enzyme as described in the protocol outlined in (Belton et al. 2012).
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description Proximal limb mouse E12.5_del1-13d9lac_HiC
Data processing Reads were mapped, filtered and bias corrected as described before (Lajoie et al. Methods 2015, Giorgetti Nature 2016).
Briefly, read pairs were mapped independently, starting at 25bp and iterated every 5bp using bowtie2 (version 2.2.4 (Langmead et al. 2009)) (as described in Imakaev Nature methods 2012) with parameter: --very-sensitive, either on mouse genome (mm10), or on the mutant genomes generated in silico. Each read was assigned to a fragment using the 5’ mapped-position shifted 3 bp toward the 3’ position to assign correctly the reads overlapping the cutting sites. The fragment assignment and mapping strand from R1 and R2 was combined and used to filter out the single-side mapped pairs, dangling-end pairs, error pairs and self-circle pairs. For each condition (same tissue and same genotype), two replicates were merged (fifteen replicates for CH12) and the interactions were filtered to discard duplicates. Each fragment was assigned to a bin (40 or 20kb) based on the position of the middle of the fragment and each valid interaction was assigned to a couple pair of bins (one bin for the R1 and one bin for the R2) and reported in the raw matrix. Prior to the ICE normalization (Imakaev et al. 2012), the rows and columns were masked if the sum of reads in this region was 10 fold less the expectation with uniform coverage, or if the number of fragments covered by at least two reads in this region was less than half the number of the fragments of this region.
Genome_build: mm10 (for DL_Wt, PL_Wt, DL_delattP-Rel5d9lac, PL_delattP-Rel5d9lac, CH12 and mESC) and mutant genomes (for DL_delattP-Rel5d9lac, PL_delattP-Rel5d9lac, DL_del1-13d9lac and PL_del1-13d9lac which are available at DOI: 10.6084/m9.figshare.5220637)
Supplementary_files_format_and_content: validPair.txt.gz contains every valid pair (not asigned to the same fragments) for each dataset. Each line is a read, column 2 is the chromosome name of the first read, column 3 is the coordinate of this read, column 4 is the strand, column 5 is the read name, column 6 is the fragment number to which this read has been asigned, columns 8-12 are the same for the other read. This file is not filtered for duplicates. __txt.tar contains all cis matrices of interactions in one folder for each resolution (20kb or 40kb bin size) and then one subfolder for the raw and one subfolder for the iced (normalised) matrices. At the 40kb resolution, cis interactions for all chromosomes are provided. At 20kb resolution, only the matrices for chr2 are provided.
 
Submission date Jul 20, 2017
Last update date May 15, 2019
Contact name Eddie Rodríguez-Carballo
E-mail(s) edgardo.rodriguez@unige.ch
Organization name Université de Genève
Department Department of Genetics and Evolution
Street address 4, Boulevard d'Yvoy
City Geneva
ZIP/Postal code 1205
Country Switzerland
 
Platform ID GPL21103
Series (2)
GSE101715 A TAD boundary at the HoxD locus segregates opposing limb regulatory landscapes and their target genes [Hi-C]
GSE101717 A TAD boundary at the HoxD locus segregates opposing limb regulatory landscapes and their target genes
Relations
BioSample SAMN07374545
SRA SRX3024413

Supplementary file Size Download File type/resource
GSM2713719_PL_HiC_E12_del1-13d9lac.validPair.txt.gz 1.5 Gb (ftp)(http) TXT
GSM2713719_PL_HiC_E12_del1-13d9lac_txt.tar.gz 210.5 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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