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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 09, 2023 |
| Title |
Capture_HiC, EV control replicate 1, library 1 |
| Sample type |
SRA |
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| Source name |
R1 mESCs
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| Organism |
Mus musculus |
| Characteristics |
cell line: R1 mESCs
cell type: mouse embryonic stem cells
developmental stage: E3.5
strain: mixture of 129S1/SvImJ and 129X1/SvJ
genotype: EV control
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryonic forebrains were dissociated into a single-cell suspension using the Papain Dissociation System (Worthington LK003150) by incubating 45 min at 37°C. Both the Cells from E16.5 forebrains and mESCs were crosslinked with 2% formaldehyde for 10 min and quenched using 0.4M glycine for 5 min.
Hi-C libraries were constructed using the Arima-HiC kit (Arima, A510008) according to the manufacturer’s protocol (Arima, A160134 v01). Probes were designed to cover the Pcdh locus and nearby genomic regions (mm10, chr18: 36,630,000-38,080,000) using the SureSelect DNA tool of Agilent SureDesign with the following settings: 2X tiling density, moderately stringent masking, and optimized performance for HS2/XT. The Capture Hi-C libraries were obtained by fast hybridization for 90 min with probes, followed by capture, washes and post-capture amplification using the SureSelect XT HS2 DNA Target Enrichment Kit (Agilent, G9987A) according to the protocol (Agilent, G9983-90000).
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Arima-HiC followed by Capture
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| Data processing |
Mouse genome (mm10) fragments were generated using the “digest_genome” tool in HiC-Pro utilities with restriction motifs “GATC” and “G^ANTC”. Raw fastq reads were cleaned using Trimmomatic (v0.38) to remove sequencing adaptors and low-quality bases from both ends with the parameters “LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25”. HiC-Pro pipelines (v2.11.4) were then used with above genome fragments and the parameter “LIGATION_SITE = GATCGATC, GANTGATC, GANTANTC, GATCANTC” to generate valid interaction pairs and contact maps.
Assembly: mm10
Supplementary files format and content: tab-delimited text files for valid interaction pairs (.allValidPairs.gz).
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| Submission date |
May 07, 2023 |
| Last update date |
May 09, 2023 |
| Contact name |
Jinpu Jin |
| Organization name |
NICHD
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| Lab |
Section on Mammalian Development and Evolution
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| Street address |
Building 6B, Room 2B-211, 6 Center Drive
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| City |
Bethesda |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE231864 |
Capture Hi-C in (EV and ZFP661-3HA OE) mESCs and E16.5 mouse forebrains |
| GSE231869 |
Modulation of CTCF barrier permeability by ZFP661 enhances protocadherin diversity for proper cortical dendritic projection in mammals |
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| Relations |
| BioSample |
SAMN34992365 |
| SRA |
SRX20248421 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7305315_Capture_HiC_EV_control_replicate_1_L1.allValidPairs.txt.gz |
116.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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