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| Status |
Public on Feb 02, 2024 |
| Title |
MD6, H3K27ac, HiChIP |
| Sample type |
SRA |
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| Source name |
MD6
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MD6
cell type: metastasis-derived cell line
chip antibody: H3K27ac (ab4729, abcam)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
HiChIP was performed as described (Mumbach et al., 2016) with some modifications. Briefly, ChIP protocol was replaced with the one reported in Crispatzu et al., 2021, using H3K27ac antibody (Abcam #ab4729), starting from 1*10 6 cells per condition. Digestion and ligation were performed overnight (NEB T4 Ligase, #M0202 instead of Invitrogen T4, 15224-041) and DNA was extracted with phenol-chlorophorm.
After biotin pull-down, beads were resuspended in 25 μL of 2X TD Buffer, 0.5uL of Tn5 (Illumina #1503861), and water to 50 μL. After transposition, beads were resuspended in 50 µL of Phusion HF 2× (New England Biosciences). Generally, 14 cycles were used for Tn5 Nextera PCR amplification (Illumina Nextera DNA UD Indexes Kit) with the following PCR program: 72 °C for 5 min, 98 °C for 1 min, then cycle at 98 °C for 15 s, 63 °C for 30 s, and 72 °C for 1 min. 50ul of PCR product were size-selected with 25ul Ampure XP Beads and separated on a magnet. The supernatant was incubated again with 90ul Ampure XP Beads. The supernatant was then discarded, beads were combined, washed with Ethanol and eluted in 30ul of Elution buffer. 1ul was loaded onto D1000 Screen Tape (TapeStation) for a second size check, where library size and molarities were extracted. Then, qPCR was performed with standard Illumina primers in order to quantify the libraries. Finally, samples were pooled with different Index/Adapter sequences and sequenced on a NovaSeq 6000
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
HiChIP sequencing reads were pre-processed, aligned and filtered using HiC-Pro (Servant et al., 2015).
We specified the genome assembly (hg19) and the restriction fragment coordinates file for the enzyme used in the processing of the samples (DpnII), while all the other parameters were kept with default values.
Filtered reads were then used as input to FitHiChIP (Bhattacharyya et al., 2019) for the identification of interacting regions.
Since ChIP-seq peaks were not available for these experiments, we used ATAC-seq ones as reference to improve accuracy of loop calling.
Loops were identified at different resolutions (bin sizes of 10 and 25 kb) and we used both peak to peak and peak to nonpeak loops for background modeling together with the coverage bias regression to assess the significance of identified interactions. Peaks with a q-value < 0.01 were considered significant.
Assembly: hg19
Supplementary files format and content: bedpe files showing interactions with a 10kb- and 25kb-resolution
Library strategy: HiChIP
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| Submission date |
Aug 19, 2022 |
| Last update date |
Feb 02, 2024 |
| Contact name |
CIBIO Zippo |
| E-mail(s) |
alessio.zippo@unitn.it
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| Organization name |
University of Trento
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| Department |
Cellular, Computation and Integrative Biology (CIBIO)
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| Lab |
Chromatin Biology & Epigenetics
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| Street address |
via sommarive 9
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| City |
Trento |
| State/province |
Not Applicable |
| ZIP/Postal code |
38123 |
| Country |
Italy |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE211607 |
Oncogenic enhancers prime quiescent metastatic cells to escape NK immune surveillance by eliciting a transcriptional memory [HiChIP] |
| GSE211610 |
Oncogenic enhancers prime quiescent metastatic cells to escape NK immune surveillance by eliciting a transcriptional memory |
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| Relations |
| BioSample |
SAMN30409809 |
| SRA |
SRX17148266 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6481393_MD6-H3K27ac_10kb.interactions_FitHiC_Q0.01.bedpe.gz |
209.5 Kb |
(ftp)(http) |
BEDPE |
| GSM6481393_MD6-H3K27ac_25kb.interactions_FitHiC_Q0.01.bedpe.gz |
358.2 Kb |
(ftp)(http) |
BEDPE |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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