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Sample GSM5603471 Query DataSets for GSM5603471
Status Public on Feb 04, 2022
Title HiC1_29781_eco1-aa_wpl1
Sample type SRA
Source name eco1-aa wpl1Δ
Organism Saccharomyces cerevisiae
Characteristics ploidy: Diploid
cell cycle stage: Meiotic prophase I
background strain: SK
genotype: RPL13A-2xFKBP12 fpr1-delta tor1-1 ndt80-delta Eco1-FRB-GFP wpl1-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: 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:
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
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)
GSE185017 Chromosome conformation for wild type, eco1-aa, wpl1Δ and eco1-aa wpl1Δ strains arrested in meiotic prophase I
GSE185021 Eco1-dependent cohesin acetylation anchors chromatin loops and cohesion to define functional meiotic chromosome domains
BioSample SAMN21900196
SRA SRX12403781

Supplementary file Size Download File type/resource 6.3 Mb (ftp)(http) COOL
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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