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| Status |
Public on Dec 07, 2011 |
| Title |
Pellet_15min_(Pellet_20110428_5) |
| Sample type |
SRA |
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| Source name |
input DNA
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: Sby2688
medium: YEPD grown:OD=0.8
antibody: none
sample type: Insoluble MNase-protected DNA fragments, 15 minute digestion
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Yeast nuclei were prepared as described [Furuyama, S., and Biggins, S. (2007), Centromere identity is specified by a single centromeric nucleosome in budding yeast, Proc Natl Acad Sci USA 104, 14706-14711], flash-frozen in liquid nitrogen and stored at -80oC. Nuclei were thawed at room temperature and digested with MNase followed by chromatin preparation as described [Furuyama and Biggins, (2007)], except that after MNase digestion, the slurry was passed four times through a 20 guage needle, then four times through a 26 guage needle [Jin, C., and Felsenfeld, G. (2007), Nucleosome stability mediated by histone variants H3.3 and H2A.Z, Genes Dev 21, 1519-1529].DNA from insoluble pellet was extracted using a standard protocol [Mito, Y., Henikoff, J., and Henikoff, S. (2005), Genome-scale profiling of histone H3.3 replacement patterns, Nat Genet 37, 1090-1097]. A modified Illumina Solexa library protocol was used as described in supplementary file Solexa_library_protocol_GEO.pdf.
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| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Insoluble MNase-protected DNA fragments, 15 minute digestion
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| Data processing |
1. We used Novoalign to map paired-end reads to release 61 (UCSC sacCer2) of the S.cervisiae genomic sequence obtained from downloads.yeastgenome.org. 50bp reads were trimmed to 25bp. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file Pellet_20110428_5..sam) Because the DNA sample was pooled with DNA from Drosophila melanogaster, we removed all paired reads that mapped to both organisms. 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file Pellet_20110428_5..wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.
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| Submission date |
Jul 05, 2011 |
| Last update date |
Jun 11, 2013 |
| 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
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| 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 |
GPL13821 |
| Series (1) |
| GSE28298 |
Tripartite organization of centromeric chromatin in budding yeast |
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| Relations |
| BioSample |
SAMN02198245 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM754389.wig.gz |
41.4 Mb |
(ftp)(http) |
WIG |
| GSM754389_Pellet_20110428_5.bam |
393.6 Mb |
(ftp)(http) |
BAM |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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