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| Status |
Public on Feb 04, 2022 |
| Title |
HiC2_28841_clb5_clb6 |
| Sample type |
SRA |
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| Source name |
clb5 clb6
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
ploidy: Diploid
cell cycle stage: Meiotic prophase I
background strain: SK1
genotype: ndt80-delta clb5-delta clb6-delta
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| Treatment protocol |
Cells were fixed and lysed as in Belton & Dekker (2015) DOI: 10.1101/pdb.prot085209. Briefly, 50 ml of cells at OD~1.8 carrying ndt80 deletion were arrested in meiotic prophase I, fixed with 3% formaldehyde for 20 minutes at 25 ˚C at 250 rpm and the reaction was quenched for 5 minutes by the addition of 0.35 M glycine (final concentration). Cells were washed with cold water, resuspended in 5 ml 1x NEBuffer 2 and frozen in liquid nitrogen.
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| Growth protocol |
Cells were grown to saturation in YPDA media before transfer to pre-sporulation media (BYTA). Cells were grown to for approx. 16 hours to OD(600) of approx. 4. Cells were diluted to OD(600) = 1.8 and sporulated for 6 hours in SPO media (0.3% Kac) to arrest in prophase I.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were prepared by grinding the frozen pellet in a chilled mortar with a pestle for 15 minutes and 1/10th of the initial pellet weight (~0.5 g) was taken for further processing. Restriction enzyme digestion (DpnII), filling-in, ligation, crosslink reversal, DNA concentration and purification and biotin removal were carried out as described in Schalbetter et al. (2018) doi: https://doi.org/10.1101/442038. DNA was then fragmented on a Bioruptor Plus sonication device (Diagenode) for a total of 2x 30 cycles 30 seconds on/off at High setting.
DNA end repair and A-tailing using T4 DNA polymerase, T4 Polynucleotide Kinase and Klenow fragment DNA polymerase I were carried out as in Schalbetter et al., 2018. Hi-C libraries were fractionated using Ampure XP beads as previously described in Belton et al. (2015) DOI: 10.1101/pdb.prot085209. Biotin pull-down, adapter ligation (NextFlex, Bioo Scientific) and sequencing (EMBL Core Genomics Facility, Heidelberg, Germany) were carried as in Schalbetter et al. (2018) doi: https://doi.org/10.1101/442038.
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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 |
Fastq reads aligned to S.cerevisiae SK1 using HiC-Pro v2.11.4 , bowtie2 v2.3.4.1 (--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder), removing singleton, multi hit, MAPQ<10 and duplicated reads.
Valid interaction pairs were converted into the .cool contact matrix format using cooler v0.7.11 (1 kb resolution)
Matrixes balanced using Iterative correction
Genome_build: S.cerevisiae SK1
Supplementary_files_format_and_content: Cooler .cool matrix 1kb binned, balanced with iterative correction
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| Submission date |
Sep 29, 2021 |
| Last update date |
Feb 04, 2022 |
| Contact name |
Daniel Robertson |
| E-mail(s) |
daniel.robertson@ed.ac.uk
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| Organization name |
University of Edinburgh
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| Department |
Discovery Research Platform for Hidden Cell Biology
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| Lab |
Bioinformatics Core
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| Street address |
2.28 Michael Swann Building, Kings Buildings, Mayfield Road
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| City |
Edinburgh |
| State/province |
Midlothian |
| ZIP/Postal code |
EH9 3JR |
| Country |
United Kingdom |
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| Platform ID |
GPL19756 |
| Series (2) |
| GSE185016 |
Chromosome conformation for wild type and clb5 clb6 strains arrested in meiotic prophase I |
| GSE185021 |
Eco1-dependent cohesin acetylation anchors chromatin loops and cohesion to define functional meiotic chromosome domains |
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| Relations |
| BioSample |
SAMN21899830 |
| SRA |
SRX12403684 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5603467_HiC2_28841_clb5_clb6_SK1_1kb.cool.gz |
12.4 Mb |
(ftp)(http) |
COOL |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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