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| Status |
Public on Jul 12, 2017 |
| Title |
Hi-C late 2-cell rep3 |
| Sample type |
SRA |
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| Source name |
Preimplantation embryo
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N x PWK/PhJ
developmental stage: late 2-cell
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| Treatment protocol |
Embryos were collected from C57BL/6N mice induced to superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours apart and mated to PWK males.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
After removing the zona pellucida, embryonic cells were washed with PBS and fixed with 1% formaldehyde for 10min at RT.
HiC libraries were prepared using sisHi-C similar with in situ Hi-C method developed by Rao et al.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Library strategy: HiC-seq
Basecalls performed using CASAVA version 1.8
Hi-C reads are processed using HiCPro version2.7.1b and replicates of same stage were pooled together
Compartment analysis are done as previously described. (Dixon et al., 2015)
TAD calling is done using Insulation score method as previously described ( Crane et al., 2015)
RNA-Seq reads were aligned to the mm9 genome assembly using Tophat version 2.0.11, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format ; read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]
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| Submission date |
Dec 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhenhai Du |
| E-mail(s) |
duzhenhai93220@gmail.com
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| Organization name |
Tsinghua University
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| Street address |
Qinghua Yuan, Haidian District
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| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE82185 |
Allelic reprogramming of 3D chromatin architecture during early mammalian development |
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| Relations |
| BioSample |
SAMN06168130 |
| SRA |
SRX2437866 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2434082_late_2cell_rep3_allValidPairs.txt.gz |
1.8 Gb |
(ftp)(http) |
TXT |
| GSM2434082_late_2cell_rep3_maternal_allValidPairs.txt.gz |
701.4 Mb |
(ftp)(http) |
TXT |
| GSM2434082_late_2cell_rep3_paternal_allValidPairs.txt.gz |
559.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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