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| Status |
Public on Nov 20, 2023 |
| Title |
HaCaT_Tet-on-Ikzf1, Dox Day3 |
| Sample type |
SRA |
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| Source name |
HaCaT
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HaCaT
cell type: Keratinocyte
genotype: Tet-on-Ikzf1 (pTet-on-Advanced, pTRE-Tight-Ikzf1)
treatment: Treated with 0.1μg/ml Dox for 3 days
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| Treatment protocol |
Doxycycline (Dox) was added into the culture medium to a final concentration of 0.1μg/ml to induce the expression of IKAROS (HaCaT_Tet-on-Ikzf1) or Luciferase (HaCaT_Tet-on-Luc).
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| Growth protocol |
The HaCaT keratinocyte cells were grown at 37 °C in DMEM medium supplemented with 10% ‘Tet System Approved FBS’ (Clontech), penicillin (100 units/ml) and streptomycin sulfate (100 μg/ml) in humidified atmosphere of 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% formaldehyde at RT for 10 minutes, and then quenched by the addition of 0.125 M glycine for 10 minutes. Cells were then washed with ice-cold PBS, snap frozen and stored at -80C before use.
In situ Hi-C was performed following the established protocol (Rao et al., 2014) with minor modifications. Briefly, nuclei were permeabilized, and DNA was digested overnight with 100 U DpnII. The ends of the restriction fragments were labeled using biotin-14-dATP and then ligated in a 1.2 mL final volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ~400 bp with a Covaris E220 evolution instrument (Covaris, Woburn, MA). Ligation junctions were then pulled down with streptavidin beads, and DNA fragments were end-repaired, dA-tailed and Illumina adapters ligated. Libraries were produced by 8 cycles of PCR amplification with KAPA Hifi DNA polymerase (Roche). The Hi-C libraries were size selected with AMPure XP beads and sequenced in house with an Illumina NEXTseq550 system and a Novaseq 6000 system at the Knapp Center for Biomedical Discovery, University of Chicago.
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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 |
instrument model: Illumina NEXTseq550 and Novaseq6000
Sequencing reads were aligned to the human hg19 assembly and processed into normalized contact maps with the HiC-Pro 2.8.0 pipeline (Servant et al., 2015) on the DNAnexus platform.
Default settings were used to remove duplicate reads, assign reads to restriction fragments, filter for valid pairs, and generate raw and ICE normalized interaction matrices at a range of resolutions.
For visualization by Juicebox (v1.11.08) valid pairs were converted to .hic files using the script “hicpro2juicebox.sh”.
Assembly: hg19
Supplementary files format and content: hic
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| Submission date |
May 07, 2023 |
| Last update date |
Nov 20, 2023 |
| Contact name |
Katia Georgopoulos |
| E-mail(s) |
katia.georgopoulos@cbrc2.mgh.harvard.edu
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| Phone |
617-7264445
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| Organization name |
Harvard Medical School
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| Department |
CBRC
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| Lab |
Georgopoulos
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| Street address |
1st and 13th St
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| City |
Charlestown |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE231878 |
A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS [Hi-C_HaCaT] |
| GSE232490 |
A multiscale 3D chromatin architecture that controls development of the humoral immune system is assembled by IKAROS |
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| Relations |
| BioSample |
SAMN34992892 |
| SRA |
SRX20249046 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7305484_HiC_HaCaT_Ik_Dox_D3.hic |
1.2 Gb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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