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Sample GSM1847483 Query DataSets for GSM1847483
Status Public on Aug 17, 2015
Title Spar_A_40
Sample type SRA
 
Source name meiotic culture
Organism Saccharomyces paradoxus
Characteristics strain: YPS138
meiotic time-point: 4 hr in meiosis
Growth protocol Cells were grown in YPA (1% yeast extract, 2% Bacto Peptone, 1% potassium acetate) for 14 hr at 23°C, harvested, resuspended in 1% potassium acetate, 0.2 × supplements (2 μg/mL adenine, 2 μg/mL histidine, 6 μg/mL leucine, 2 μg/mL tryptophan, 2 μg/mL uracil) and sporulated at 23°C.
see SAMPLES section
Extracted molecule genomic DNA
Extraction protocol Based on Pan et al. 2011 Cell 144:719-731. Samples were harvested at the indicated time-points after transfer to sporulation conditions, crosslinked with 1% formaldehyde, spheroplasted, chromatin extracted, treated with a dilution series of micrococcal nuclease (MNase) from 5 to 80 units, and DNA purified, as described in Pan et al. 2011. Mononucleosome-sized DNA was then purified by size fractionation on agarose gels and libraries prepared for Illumina sequencing.
 
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina HiSeq 2500
 
Description digested with 40 units Mnase
Data processing Reads were first clipped to remove any Illumina adapter sequences present and reads shorter than 35 bp were discarded (both ends of paired end reads were discarded). The clipped reads were then mapped to the proper target genome using BWA MEM (default options). The output SAM files were coordinate sorted and read groups added and merged into single sample BAM files using the PICARD toolkit. The output BAM files were then post-processed with a series of custom scripts to filter for uniquely mapping and properly paired reads. Proper pairing was defined as reads where the chromosome of each pair is the same, insert size was less than 250 bp, and strands were in opposite/inward orientation (==> <==). This was done using bedtools to convert the BAM files to Paired BED files (bedpe) and then filtering. The filtered read pairs were used to compute genome-wide coverage using the bedtools genomecov program.
Reads were mapped to each species'/strains' specific genome assembly.
Genome_build: For wild-derived S. cerevisiae strains YPS128 and UWOPS03-461.4, reads were mapped to the SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645; for S. paradoxus YPS138, reads were mapped to the strain's genome assembly from SGRP (Saccharomyces Genome Resequencing Project, Wellcome Trust Sanger Institute); for S. mikatae IFO1815 and S. kudriavzevii ZP591, reads were mapped to the strains' genome assemblies from Scannell et al. 2011 G3 1: 11-25, available on http://www.saccharomycessensustricto.org.
Supplementary_files_format_and_content: Tab delimited text files include raw paired-end coverage map at each base position in the genome (reads were extended to mononucleosome DNA length, then occupancy calculated by summing at each base pair the number of extended reads that overlapped that base pair)
 
Submission date Aug 11, 2015
Last update date May 15, 2019
Contact name Isabel Lam
Organization name Memorial Sloan Kettering Cancer Center
Department Molecular Biology
Lab Keeney Lab
Street address 1275 York Avenue
City New York
State/province New York
ZIP/Postal code 10065
Country USA
 
Platform ID GPL20787
Series (2)
GSE71929 Whole-genome nucleosome mapping in meiotic diploid Saccharomyces species (S. paradoxus, S. mikatae, S. kudriavzevii) and wild-derived S. cerevisiae strains (YPS128, UWOPS03-461.4)
GSE71930 Non-paradoxical evolutionary stability of the recombination initiation landscape in Saccharomycetes
Relations
BioSample SAMN03980010
SRA SRX1141324

Supplementary file Size Download File type/resource
GSM1847483_20150728-Spar_A_40.txt.gz 30.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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