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| Status |
Public on Jan 04, 2023 |
| Title |
MC_HiC_rep2 |
| Sample type |
SRA |
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| Source name |
chondrocytes
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: wt
cell_type: Meckel's cartilage
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
E14.5 Meckel’s cartilage bars were dissected from wild-type C57BL/6J mouse embryos as previsouly described (Ishizeki, 1996 & Wiszniak, 2015) with modifications. E14.5 forelimb was dissected from wild-type mouse embryos with removal of surrounding connective tissues. Dissected forelimb cartilage was then digested following the same procedure as the digestion of Meckel’s cartilage.
Briefly, cells were crosslinked in 1% formaldehyde for 10 mins at room temperature and quenched with 0.2M glycine. Cells were pelleted, washed with 1ml HBSS and then resuspended with 1ml ice-cold Hi-C lysis buffer, incubated on ice for 30min and were further dounced with pestles to insure complete lysis. Chromatin was then opened up at the presence of 0.5% SDS at 65°C for 5 mins and quenched with Triton X-100 at the final concentration of 1%. Samples were then digested overnight with DpnII at 37°C on a thermomixer with interval shaking, followed by heat inactivation of DpnII and fill-in of the restriction fragment overhangs. Samples were then ligated with T4 DNA ligase at 16°C for 4hr, and crosslink reversal was performed by Proteinase K digestion. 3C libraries were then extracted and purified by phenol-chloroform isoamyalcohol extraction and ethonal precipitation. Efficiency of digestion and ligation was assessed by gel electrophoresis of quality controls. 3C libraries were then sheared to 200-700bp by Covaris sonication and Dynabeads MyOne Streptavidin T1 was used to perform biotin pull-down after washing. End repair, dA-tailing and ligation of libraries were performed with NEBNext Ultra II Ligation Module. Libraries was amplified on the streptavidin beads using Phusion DNA Polymerase, size-selected with AMPure XP beads, quantified by Qubit dsDNA High Sensitivity Assay and then sequenced on the NovaSeq platform.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
E14.5 Meckel's cartilage Hi-C replicate2
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| Data processing |
Fasqt files of Hi-C samples were processed with Trim galore to remove low-quality reads and adapters.
Adaptor-trimmed Hi-C data were mapped to mm10 iteratively with bowtie2.
Mapped sequences were parsed into a Python data structure and assigned to DpnII fragments. HiC dataset object was created after fragment filtering, and generated hdf5 files were transformed to cool format with cooler cload hiclib and then balanced with cooler balance.
mm10
cool
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| Submission date |
Oct 04, 2021 |
| Last update date |
Jan 04, 2023 |
| Contact name |
Qian Bian |
| E-mail(s) |
qianbian@shsmu.edu.cn
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| Phone |
86-21-3845-2656
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| Organization name |
Shanghai Jiao Tong University School of Medicine
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| Department |
Shanghai Institute of Precision Medicine, Ninth People’s Hospital
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| Street address |
Jinzun Road No.115
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| City |
Shanghai |
| ZIP/Postal code |
200011 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE185255 |
Integration of 3D genome architecture and local chromatin features uncovers enhancers underlying craniofacial-specific cartilage defects |
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| Relations |
| BioSample |
SAMN22039266 |
| SRA |
SRX12475686 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5608842_MC_HiC_rep2_10kb.cool.gz |
171.1 Mb |
(ftp)(http) |
COOL |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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