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Status |
Public on Aug 17, 2015 |
Title |
Spar_A_40 |
Sample type |
SRA |
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Source name |
meiotic culture
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Organism |
Saccharomyces paradoxus |
Characteristics |
strain: YPS138 meiotic time-point: 4 hr in meiosis
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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
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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.
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Library strategy |
MNase-Seq |
Library source |
genomic |
Library selection |
MNase |
Instrument model |
Illumina HiSeq 2500 |
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Description |
digested with 40 units Mnase
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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)
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Submission date |
Aug 11, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Isabel Lam |
Organization name |
Memorial Sloan Kettering Cancer Center
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Department |
Molecular Biology
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Lab |
Keeney Lab
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Street address |
1275 York Avenue
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City |
New York |
State/province |
New York |
ZIP/Postal code |
10065 |
Country |
USA |
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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 |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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