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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 19, 2021 |
| Title |
MCF7_HiMeDIP |
| Sample type |
SRA |
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| Source name |
MCF7
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
antibody: anti-5-methylcytosine (Active Motif 61479)
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| Growth protocol |
E14 ESCs were grown in DMEM GlutaMAX supplemented with 15% FBS, non-essential amino acids, 50μM 2-mercaptoethanol, antibiotic-antimycotic and 1,000 U/ml LIF. MCF7 and 2102Ep cells were grown in DMEM GlutaMAX supplemented with 10% FBS, penicillin-streptomycin and non-essential amino acids.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% formaldehyde for 12 minutes. Chromatin was digested in situ using 2,750 U of DpnII overnight on ~5 million cells permeabilised with 0.3% SDS. After a fill-in reaction containing biotinylated dATP, ends were ligated with 2,000 of T4 DNA ligase. Purified DNA was sonicated to 300-700 bp, and sequencing adaptors ligated using NEBnext Ultra II reagents. After heat denaturation, methylated DNA was immunoprecipitated using an anti-5mC antibody (Active Motif 61479). Immunoprecipitated DNA was purified, followed by isolation of ligated fragments using streptavidin beads, and library amplification.
Libraries were prepared using the NEBNext ultra II DNA library prep kit.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Library strategy: HiChIP
Reads were aligned using PAtChER (https://github.com/MBrancoLab/PAtChER), with -d 20000 for human data and -d 10000 for mouse data.
Read pairing information was removed using PAtChER's unpair tool.
BigWig tracks were generated using the bamCoverage function of deepTools2.0, with CPM normalisation.
Normalised bigWig tracks were generated by dividing the HiChIP tracks by the corresponding Hi-C tracks, using bigwigCompare (deeptools) with --pseudocount 0.01 --skipZeroOverZero.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: BigWig tracks
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| Submission date |
Aug 17, 2021 |
| Last update date |
Aug 21, 2021 |
| Contact name |
Miguel R Branco |
| E-mail(s) |
m.branco@qmul.ac.uk
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| Organization name |
Blizard Institute
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| Street address |
4 Newark Street
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| City |
London |
| ZIP/Postal code |
E1 2AT |
| Country |
United Kingdom |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE182304 |
Locus-specific chromatin profiling of evolutionarily young transposable elements [HiChIP] |
| GSE182306 |
Locus-specific chromatin profiling of evolutionarily young transposable elements |
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| Relations |
| BioSample |
SAMN20839642 |
| SRA |
SRX11802723 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5526449_MCF7_HiMeDIP.bw |
133.4 Mb |
(ftp)(http) |
BW |
| GSM5526449_MCF7_normalised.bw |
198.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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