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| Status |
Public on Nov 15, 2011 |
| Title |
PolII_80mMsalt_control_(IP1_Ctl_20110313_1) |
| Sample type |
SRA |
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| Source name |
Pol II ChIP
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: S2 cells
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was done as described in CM Weber, JG Henikoff & S Henikoff, H2A.Z nucleosomes enriched over active genes are homotypic, Nat Struct Mol Bio 2010 Dec;17(12):1500-7, PMID 21057526 and supplementary file ChIP_protocol.rtf. A modified Illumina Solexa library protocol was used as described in supplementary file Solexa_library_protocol_GEO.pdf.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
supplementary protocol file: Solexa_library_protocol_GEO.pdf
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| Data processing |
1. We used Novoalign to map paired-end 25bp reads to release r5.30 of the D.melanogaster genomic sequence obtained from FlyBase. The genomic sequence was unmasked and chrU, chr2RHet, chr2LHet, chr3RHet, chr3LHet, chrXHet and chrYHet were omitted from the reference sequence. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file PolII_80mMsalt_control_20110313_1.sam) 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 PolII_80mMsalt_control_20110313_1.bedgraph) 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 18, 2011 |
| Last update date |
Dec 18, 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 |
GPL13304 |
| Series (1) |
| GSE30755 |
Genome-wide reductions in active chromatin, paused RNA Polymerase II and nucleosome turnover during heat shock |
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| Relations |
| BioSample |
SAMN02198182 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM763037.bedgraph.gz |
101.8 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM763037.sam.gz |
1.9 Gb |
(ftp)(http) |
SAM |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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