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| Status |
Public on May 01, 2024 |
| Title |
WT_hCNCC_PC_HiC |
| Sample type |
SRA |
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| Source name |
H9-derived cranial neural crest cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: H9-derived cranial neural crest cells
cell type: Stem cells
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were first fixed with 2% formaldehyde for 10 minutes at ambient temperature, followed by quenching with 0.2M glycine for 5 minutes. Post-fixation, cells were lysed, and endogenous nucleases were inactivated with 0.3% SDS. Chromatin was digested using 100U of HindIII (New England Biolabs), labeled with biotin-14-dCTP (Invitrogen), and then ligated using 50U of T4 DNA ligase (New England Biolabs). After reversing the cross-links, DNA was isolated using the QIAamp DNA Mini Kit (Qiagen), in strict accordance with the manufacturer's instructions. Subsequent steps involved fragmenting the DNA to 300-600 bp, end-repair, A-tailing, and adapter ligation using SureSelect adaptors. Biotinylated fragments were isolated through streptavidin-affinity pull-down and PCR amplified.
Promoter-specific Capture Hi-C was performed using the SureSelect XT Library Prep Kit ILM (Agilent Technologies), which included a custom-designed biotinylated RNA bait library and paired-end blockers. Post-capture PCR enrichment was followed by final purification of the libraries with AMPure XP beads (Beckman Coulter). Library quality was evaluated using Bioanalyzer profiles (Agilent Technologies), and high-throughput sequencing was performed on the Illumina NovaSeq 6000 platform.
promoter capture HiC
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Capture Hi-C data of human cranial neural crest cells (hCNCCs), a genome digest file for HindIII was created using hicup_digester. The HiCUP software (version 0.9.2) was then employed to generate alignment files. To prepare files for the Chicago R package (version 1.30.0), scripts such as bam2chicago.sh and makeDesignFiles.py from chicagoTools were utilized. The Chicago package produced washU_text format results, showcasing interactions between two genomic positions. Interactions with a score bigger than 5 were considered high-confidence and visualized as arcs using pygenometrack (version 3.9)
Assembly: hg19
Supplementary files format and content: tab-delimited genomic regions interacted with gene promoters
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| Submission date |
Apr 02, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Xu Xiaopeng |
| E-mail(s) |
xu_xiaopeng@gzlab.ac.cn
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| Organization name |
Guangzhou National Laboratory
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| Street address |
96 Xingdao South Road, Guangzhou International Bio Island, Haizhu District
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| City |
Guangzhou |
| ZIP/Postal code |
510320 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE263085 |
Auricular Malformations Driven by Copy Number Variations in a Hierarchical Enhancer Cluster and Dominant Enhancer Recapitulates Human Pathogenesis [PC-HiC] |
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| Relations |
| BioSample |
SAMN40731352 |
| SRA |
SRX24137117 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8185639_WT_hCNCC_PC_HiC_washU_text.arcs.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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