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| Status |
Public on Nov 15, 2011 |
| Title |
80mMsalt_DRB_HS_(Input4_20110223_8) |
| Sample type |
SRA |
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| Source name |
80mM salt fraction
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: S2 cells
treatment: Heat shock for 15min at 37C, and DRB for 10min
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Salt extraction was done as described in S Henikoff, JG Henikoff, A Sakai, GB Loeb, K Ahmad, Genome-wide profiling of salt fractions maps physical properties of chromatin. Genome Research, March 2009, 19:460-469, PMID 19088306 and supplementary file Salt_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 |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Salt extraction after 15 minutes of heat shock at 37 degrees C and DRB treatment for 10 min.
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 80mMsalt_DRB_HS_20110223_8.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 80mMsalt_DRB_HS_20110223_8.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) |
jorja@fhcrc.org
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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 |
SAMN02198178 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM763033.bedgraph.gz |
115.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM763033.sam.gz |
3.0 Gb |
(ftp)(http) |
SAM |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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