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| Status |
Public on Mar 04, 2020 |
| Title |
86_Wapl-Control |
| Sample type |
SRA |
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| Source name |
oocyte
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| Organism |
Mus musculus |
| Characteristics |
tissue: oocyte
genotype: Wapl-Control
strain: C57BL/6J
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
snHi-C protocol according to Flyamer et al., 2017
The library preparation was done by the VBCF NGS unit (vbcf.ac.at) following the standard DNA sample preparation protocol.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Description |
59603
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| Data processing |
Base calling was performed by VBCF NGS unit
Mapping: iterative mapping (see Imakaev et al, 2012) using bwa
Read filtering was performed as in Flyamer et al., 2017:
Summary of filtering: If two reads map to the same strand, and each side of the read is within 500 bp of any side of the other read, we retain only one copy of the read. We separate the genome into 500 bp bins. If any two bins are interacting more than once, only one interaction is counted. Since each region is only present in the single cell up to 4 times (in oocytes), we eliminated all 500 bp bins that form more than 8 unique interactions with other bins.
Filtered reads were then binned at different resolutions (we provide 4 resolutions) using read start as a read position and stored in the Cool file format. No normalization was applied to the data.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix of whole-genome locus interaction frequencies binned at 1kb, 10kb, 40kb, and 100kb resolutions stored in the Cool file format.
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| Submission date |
Jun 05, 2019 |
| Last update date |
Mar 05, 2020 |
| Contact name |
Kikuë Tachibana |
| Organization name |
IMBA
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| Lab |
Tachibana Lab
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| Street address |
Dr.-Bohr-Gasse 3
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| City |
Vienna |
| State/province |
--- Select a state --- |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platform ID |
GPL21626 |
| Series (1) |
| GSE132264 |
Wapl-mediated release of Scc1-cohesin regulates chromosome structure and segregation in mouse oocytes |
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| Relations |
| BioSample |
SAMN11963109 |
| SRA |
SRX5978513 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3855218_CBPYUANXX_3_59603_TCCGCGAATATAGCCT.10000.cool.gz |
796.8 Kb |
(ftp)(http) |
COOL |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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