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| Status |
Public on Jul 27, 2021 |
| Title |
23_Wapl.KO_Rec8.TEV |
| Sample type |
SRA |
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| Source name |
oocyte
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| Organism |
Mus musculus |
| Characteristics |
strain: Rec8TEV/TEVWaplfl/fl (Tg)Zp3-Cre
genotype: +TEV
developmental stage: GV oocyte - SN
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
snHi-C protocol according to Flyamer et al., 2017
The library preparation was performed following the standard DNA sample preparation protocol by the VBCF NGS unit or the NGS facility in the Department of Totipotency, MPIB
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
74931
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| Data processing |
Base calling was performed by VBCF NGS facility and NGS facility in the Department of Totipotency, MPIB
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 |
Mar 30, 2021 |
| Last update date |
Jul 27, 2021 |
| Contact name |
Bart Johan H Dequeker |
| Organization name |
IMBA - Institute of Molecular Biotechology
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| Street address |
Dr. Bohr-Gasse 3
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE171159 |
Ovulation suppression protects against chromosomal abnormalities in mouse eggs at advanced maternal age |
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| Relations |
| BioSample |
SAMN18541281 |
| SRA |
SRX10479187 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5220090_74931.10000.cool.gz |
981.0 Kb |
(ftp)(http) |
COOL |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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