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| Status |
Public on Feb 22, 2023 |
| Title |
4Cseq-hg-Control-FB-FGF8-Rep1-L21103 |
| Sample type |
SRA |
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| Source name |
Skin fibroblasts
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Skin fibroblasts
genotype: Healthy control
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Skin biopsies were collected from SHFM3 patients and controls by standard procedures. Fibroblasts were cultured in DMEM (Lonza) supplemented with 10% fetal calf serum (Gibco), 1% L-glutamine (Lonza) and 1% penicillin/streptomycin (Lonza).
For 4C-seq libraries fixation and lysis were performed as described for Capture Hi-C. After the first digestion with DpnII (NEB), sticky ends were religated in a 50 ml falcon tube (700 μl 10 ligation buffer (Fermentas), 7 ml H2O, 50 U T4 DNA ligase (Thermo); overnight at 16 °C) and DNA de-cross linked and cleaned as described for the Capture Hi-C. Next, a second digestion (150 μl sample, 50 μl 10× Csp6I buffer (Thermo), 60 U Csp6I (Thermo) 295 μl H2O; overnight at 37 °C) and another re-ligation were performed. For all viewpoints, DNA was purified using a PCR clean up Kit (Qiagen) and 1.6 μg DNA was amplified by PCR (LBX1 Viewpoint: read-primer 5′-TCTATATGCTACCATGATC-3′, secondary-primer 5′-GATGAACTGGAATACCCA-3′; FGF8 Viewpoint: read-primer 5′-AGGGTGCGTTCCAAGATC-3′, secondary-primer 5′-GGTGGCCTGGATGGAAGT-3′; BTRC Viewpoint: read-primer 5′-CAACGCAGCGCCCGGATC-3′, secondary-primer 5′-CTGGGAATGAGGACCTAGGGC-3′). For the library reaction, primers were modified with TruSeq adapters (Illumina): Adapter1 5′-CTACACGACGCTCTTCCGATCT-3′ and Adapter2 5′-CAGAC GTGTGCTCTTCCGATCT-3′. Between 50 and 200 ng were used as input of a single 4C PCR reaction depending on the complexity. The reaction was performed in a 50 μl volume using the Expand Long Template System (Roche) and 29 reaction cycles. After the PCR all reactions were combined and the DNA purified with a PCR clean up Kit (Qiagen).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Sequencing reads were mapped, normalized and smoothed with pipe4C53 using the reference genome GRCh37 and default settings. All viewpoints were performed in replicates and as quality measure >70% of reads were mapped within a size range of 1Mb and >80% within 100kb around the viewpoint.
Assembly: hg19
Library strategy: 4C-seq
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| Submission date |
Jan 22, 2023 |
| Last update date |
Feb 23, 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 |
GPL24676 |
| Series (2) |
| GSE197404 |
Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve Split-Hand/Foot Malformation type 3 |
| GSE223454 |
Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve Split-Hand/Foot Malformation type 3 [4C-seq] |
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| Relations |
| BioSample |
SAMN32868386 |
| SRA |
SRX19248038 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6956519_4Cseq-hg-Control-FB-FGF8-Rep1-L21103.bedgraph.gz |
3.2 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM6956519_4Cseq-hg-Control-FB-FGF8-Rep1-L21103.wig.gz |
1.4 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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