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| Status |
Public on Feb 22, 2023 |
| Title |
CaptureHiC-mm-Wt-FLHL-E115-tecRep1-L11678 |
| Sample type |
SRA |
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| Source name |
Embryonic Forelimb Hindlimb
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| Organism |
Mus musculus |
| Characteristics |
genotype: Wild type
embryonic stage: E11.5
strain/background: c57bl6.J
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| Treatment protocol |
The capture HiC protocol was performed as decribed in Formation of new chromatin domains determines pathogenecity of genomic duplications. Franke et al., Nature 2016.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Forelimb and hindlilmb buds were micro-dissected from E11.5 mouse embryos in 1xPBS, a single cell suspension was made using Trypsin, then samples were crosslinked using 2% PFA, snap frozen, and stored at -80 °C.
Snap frozen samples were first digested using DpnII, religated using the T4 DNA ligase (Thermo Fisher Scientific). The chimeric chromatin products were then decrosslinked overnight. RNase A treated chromatin was then precipitated.The precipiated chromatin was sheared using a Covaris sonicator (duty cycle: 10%; intensity: 5; cycles per burst: 200; time: 6 cycles of 60 s each; set mode: frequency sweeping; temperature: 4–7 °C). Adaptors were added to the sheared DNA and amplified according to the manufacturer’s instructions for Illumina sequencing (Agilent). The library was hybridized to the custom-designed SureSelect beads and indexed for sequencing following the manufacturer’s instructions (Agilent).
Capture Hi-C
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
CaptureHiC-mm9-Wt-FLHL-E115-Rep1Rep2Rep3-50bp-merged-MAPQ30-KR-5kb-L11359-L11678-S11359-L9627.WashU.txt
Virtual4C-mm9-Wt-merged-Lbx1-5kb.bedgraph
Virtual4C-mm9-Wt-merged-Btrc-5kb.bedgraph
Virtual4C-mm9-Wt-merged-Fgf8-5kb.bedgraph
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| Data processing |
In a pre-processing step, the reads in fastq files were trimmed to 50 bp, if necessary, to obtain the same initial read length for all samples. Afterwards, mapping, filtering and deduplication of paired-end sequencing data was performed using the HiCUP pipeline v0.8.1(no size selection, Nofill: 1, Format: Sanger). The pipeline was set up with Bowtie2 v2.4.2 for mapping short reads to reference genome mm9. For merging biological replicates, the final bam files produced by the HiCUP pipeline were joined.
Juicer tools v1.19.02 was used to generate binned contact maps and to normalize maps by Knights and Ruiz (KR) matrix balancing.
For the generation of cHi-C maps, only read-pairs referring to the region of interest (chr19:44,440,001-46,400,000) and with MAPQ≥30 were considered.
In order to explicitly consider the duplicated region in the Dup mutant, we created cHi-C maps by applying the copy-number variation effects (LOIC)-normalization44 (python package iced v.0.5.345) to raw count maps.
Assembly: mm9
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| Submission date |
Jan 22, 2023 |
| Last update date |
Feb 22, 2023 |
| Contact name |
Giulia Cova |
| E-mail(s) |
Giulia.cova@nyulangone.org
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| Organization name |
Max Planck Institute
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| Street address |
63-73 Ihnestrasse
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| City |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE197404 |
Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve Split-Hand/Foot Malformation type 3 |
| GSE223450 |
Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve Split-Hand/Foot Malformation type 3 [Capture Hi-C, Virtual4C] |
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| Relations |
| BioSample |
SAMN32868445 |
| SRA |
SRX19274663 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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