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| Status |
Public on Dec 04, 2014 |
| Title |
Ino80_IP_(20130401_2_2) |
| Sample type |
SRA |
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| Source name |
Ino80 IP
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell: nuclei
strain: W303 (WT)
genotype: MATa ade2-1 can1-100 his3-11, 15 leu2-3, 112 trp1-1 ura3-1 RAD5+ INO80-3FLAG-kanMX4
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclear isolation, chromatin preparation, and immunoprecipitation were performed as described (PMID 23468649). Sequencing libraries were prepared as described (PMID 22025700), except that TruSeq adapters were used for multiplexing and the ratio of sample to Ampure beads was changed from 5:9 to 1:1 in the two cleanup steps to compensate for the longer length of the TruSeq adapters.
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| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Ino80 IP, 10' MNase
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| Data processing |
1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. The Illumina sample was a mixture of yeast DNA and fly DNA so we also mapped the reads to release 5.30 of D.melanogaster (Sep 2010) obtained from FlyBase. If a read was mapped to multiple locations, one location was picked at random. 2. We extracted properly paired reads that were only mapped to yeast (Supplementary file .bed).
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| Submission date |
Jul 17, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
[email protected]
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| Phone |
206-667-4850
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| Organization name |
Fred Hutchinson Cancer Research Center
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| Department |
Basic Sciences
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| Lab |
Henikoff
|
| Street address |
1100 Fairview AV N, A1-162
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
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| Platform ID |
GPL17342 |
| Series (1) |
| GSE59523 |
Asymmetric nucleosomes flank promoters in the budding yeast genome |
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| Relations |
| BioSample |
SAMN02923724 |
| SRA |
SRX656656 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1438792_Ino80_IP.bed.gz |
28.0 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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