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| Status |
Public on Jan 03, 2024 |
| Title |
Med1313lfl_UNT_HIC_rep1 |
| Sample type |
SRA |
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| Source name |
Mouse embryonic stem cells, untreated control, Med13/13l fl/fl Hi-C
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| Organism |
Mus musculus |
| Characteristics |
cell line: Med13;Med13l flfl
strain: Rosa26::ERT2-Cre
treatment: untreated
treatment time: 0h
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| Treatment protocol |
Med13/13lfl/fl ERT2-Cre ESCs were treated with 800nM 4-hydroxytamoxifen (Sigma) for 96 hours. Pcgf4-/-/Pcgf2fl/fl ERT2-Cre ESCs were treated with 800nM 4-hydroxytamoxifen (Sigma) for 72 hours. For RA differentiation, ESCs were treated with 1µM retinoic acid (Sigma-Aldrich) for 48h.
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| Growth protocol |
Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor. HEK293T celles were grown in EC-10 medium (DMEM supplemented with 10% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.4 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor). Drosophila S2 (SG4) cells were grown adhesively at 25°C in Schneider’s Drosophila Medium (Life Technologies), supplemented with 1x penicillin-streptomycin solution (Life Technologies) and 10% heat-inactivated fetal bovine serum (Labtech).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
In-situ Hi-C in Med13/13lfl/fl ESCs was performed in biological duplicates as described in Haarhuis et al. (2017).
Hi-C libraries were sequenced on Illumina NextSeq 500 platform as 51bp or 40bp paired-reds.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Hi-C sequencing data was mapped to GRCm38.p6 and processed with Hi-C-Pro 2.9.
Further data analysis was performed with GENOVA (github.com/deWitLab/GENOVA).
Genome_build: mm10
Supplementary_files_format_and_content: validPairs files, containing the genomic position and strand of the two pairs of a Hi-C ligation
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| Submission date |
Nov 10, 2021 |
| Last update date |
Jan 03, 2024 |
| Contact name |
Robin H. van der Weide |
| Organization name |
Hubrecht Institute
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| Lab |
Kind Lab
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| Street address |
Uppsalalaan 8
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| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE185930 |
Distinct roles of CKM-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction |
| GSE188551 |
A dual role for CDK-Mediator in controlling Polycomb-dependent topology and priming genes for induction [Hi-C] |
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| Relations |
| BioSample |
SAMN23037936 |
| SRA |
SRX13103161 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5685411_MED13cKO_0h_rep1.validPairs.txt.gz |
4.8 Gb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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