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Sample GSM5603466 Query DataSets for GSM5603466
Status Public on Feb 04, 2022
Title HiC2_11633_wt
Sample type SRA
 
Source name wild type
Organism Saccharomyces cerevisiae
Characteristics ploidy: Diploid
cell cycle stage: Meiotic prophase I
background strain: SK1
genotype: ndt80-delta
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.
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.
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.
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
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
 
Submission date Sep 29, 2021
Last update date Feb 04, 2022
Contact name Daniel Robertson
E-mail(s) daniel.robertson@ed.ac.uk
Organization name University of Edinburgh
Department Discovery Research Platform for Hidden Cell Biology
Lab Bioinformatics Core
Street address 2.28 Michael Swann Building, Kings Buildings, Mayfield Road
City Edinburgh
State/province Midlothian
ZIP/Postal code EH9 3JR
Country United Kingdom
 
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
Relations
BioSample SAMN21899831
SRA SRX12403683

Supplementary file Size Download File type/resource
GSM5603466_HiC2_11633_wt_SK1_1kb.cool.gz 7.9 Mb (ftp)(http) COOL
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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