NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5608848 Query DataSets for GSM5608848
Status Public on Jan 04, 2023
Title FL_HiC_rep1
Sample type SRA
 
Source name chondrocytes
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: wt
cell_type: forelimb
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.
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description E14.5 forelimb Hi-C replicate1
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
 
Submission date Oct 04, 2021
Last update date Jan 04, 2023
Contact name Qian Bian
E-mail(s) qianbian@shsmu.edu.cn
Phone 86-21-3845-2656
Organization name Shanghai Jiao Tong University School of Medicine
Department Shanghai Institute of Precision Medicine, Ninth People’s Hospital
Street address Jinzun Road No.115
City Shanghai
ZIP/Postal code 200011
Country China
 
Platform ID GPL24247
Series (1)
GSE185255 Integration of 3D genome architecture and local chromatin features uncovers enhancers underlying craniofacial-specific cartilage defects
Relations
BioSample SAMN22039276
SRA SRX12475699

Supplementary file Size Download File type/resource
GSM5608848_FL_HiC_rep1_10kb.cool.gz 184.5 Mb (ftp)(http) COOL
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap