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| Status |
Public on Apr 17, 2024 |
| Title |
HCT116_HiC_Nut7h_BR2 |
| Sample type |
SRA |
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| Source name |
HCT116
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
treatment: Nutlin3a 7h
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed in DMEM medium supplemented with 10% FBS and 2% methanol-free formaldehyde for 10 minutes rotating at room temperature. After quenching the formaldehyde with 0.125M glycine and washing the cells with 1X PBS, nuclei were extracted by lysing the cells in 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA630 (SIGMA-ALDRICH #18896-50ML), 1× cOmplete EDTA-free protease inhibitor cocktail. Chromatin was digested overnight with HindIII enzyme and the cohesive restriction fragment ends were filled-in with dCTT, dTTP, dGTP and biotin-14-dATP(Invitrogen #19524-016) nucleotides. After blunt-end ligating the restriction fragment ends, the chromatin was decrosslinked by incubating overnight with proteinase K and purified by phenol:chloroform:isoamyl alcohol 25:24:1 (SIGMA-ALDRICH #P3803-100ML) extraction.Non-informative biotin at restriction fragment ends was removed by incubating the samples with dATP and T4 DNA polymerase (New England Biolabs#M0203S). After purifying the DNA again with a phenol:chloroform:isoamyl alcohol extraction, 10µg of the chromatin was sheared using a Covaris M220 focused ultrasonicator in 130µl cuvettes using the following parameters: 20% duty factor, 50 peak incident power, 200 cycles per burst, 65 seconds. The ends were end-repaired and dATP-tailed, followed by a biotin-pulldown using Dynabeads MyOne streptavidin C1 paramagnetic beads (Thermo Fisher #65001) to enrich for those DNA fragments which contain information of a chromatin loop. PE Illumina adapters(Supplementary Data 9) were ligated to the sample and the library was amplified for 8 cycles. Finally, the library was purified using a SPRI bead double-sided selection (0.4-1 volumes). Size and concentration of the finished Hi-C libraries was assessed by DNA ScreenTape Analysis (Agilent #5067-5582) on an Agilent 2200 Tapestation.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Various steps were taken to process the Hi-C data, including read quality control, mapping, interaction detection, filtering, and matrix normalization using the TADbit pipeline
Assembly: GRCh37.p13
Supplementary files format and content: HiC matrices .abc.txt
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| Submission date |
Jun 27, 2023 |
| Last update date |
Apr 17, 2024 |
| Contact name |
Biola M Javierre |
| E-mail(s) |
bmjavierre@carrerasresearch.org
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| Organization name |
Josep Carreras Leukaemia Research Institute
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| Lab |
3D Chromatin Organization
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| Street address |
Ctra de Can Ruti, Camí de les Escoles , s/n
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| City |
Badalona |
| State/province |
Barcelona |
| ZIP/Postal code |
08916 |
| Country |
Spain |
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| Platform ID |
GPL20795 |
| Series (2) |
| GSE235944 |
p53 rapidly restructures 3D chromatin organization to trigger a transcriptional response [HiC] |
| GSE235947 |
p53 rapidly restructures 3D chromatin organization to trigger a transcriptional response |
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| Relations |
| BioSample |
SAMN36002323 |
| SRA |
SRX20795164 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7512252_HCT116_WT_NUT_7h_BR2_hic-nrm_100.abc.txt.gz |
180.8 Mb |
(ftp)(http) |
TXT |
| GSM7512252_HCT116_WT_NUT_7h_BR2_hic-nrm_50.abc.txt.gz |
248.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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