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| Status |
Public on Jul 13, 2016 |
| Title |
MNase-Seq |
| Sample type |
SRA |
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| Source name |
Flower
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| Organism |
Zea mays |
| Characteristics |
inbred line: B73
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were prepared as described in the ChIP protocol except that EDTA was omitted from buffers. Nuclei pellet was resuspended in 500 μl Digestion Buffer (50 mM Tris-HCl pH8.0, 5 mM CaCl2, 0.1 mM PMSF, 1 µg/ml cOmplete Protease Inhibitor Cocktail (Roche, Penzberg, Germany)). Samples were sonicated for 5 second and treated with 0.02 U /µl of micrococcal nuclease (NEB, Ipswich, MA, USA) for 10 min at room temperature. The reaction was stopped with 10 mM EDTA and DNA was prepared as in the ChIP protocol. The purified DNA was separated in a 2% agarose gel and fragments ~150 bp in size were recovered. Approximately 100 ng of mononucleosome DNA was used for Illumina library construction. As a control, randomly fragmented chromatin was prepared by sonication to produce 200 - 500 bp fragments.
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| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the B73 reference genome sequence (release AGPv2) using the Burrows-Wheeler Aligner (BWA)
Data were filtered base on unique mapping
peak calling using MACS with parameter bandwidth 800
bed file were used to calculated ratio of nucleasome occupancy
Ratio calculated by treatment divided by control from peak regions
Genome_build: B73 (release AGPv2)
Supplementary_files_format_and_content: [.bed] reports peaks, counts, ratios of nucleasome occupancy
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| Submission date |
Jul 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Wojciech Pawlowski |
| E-mail(s) |
mw729@cornell.edu
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| Organization name |
Cornell University
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| Department |
Plant Breeding and Genetics
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| Street address |
Bradfield Hall, Room 403
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| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
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| Platform ID |
GPL15463 |
| Series (2) |
| GSE84368 |
Genomic features shaping the landscape of meiotic double-strand break hotspots in maize [MNase-Seq] |
| GSE84369 |
Genomic features shaping the landscape of meiotic double-strand break hotspots in maize |
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| Relations |
| BioSample |
SAMN05389328 |
| SRA |
SRX1943902 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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