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Sample GSM807109 Query DataSets for GSM807109
Status Public on Dec 05, 2011
Title Total nuclei DNA 2 (PD5_rep2_20110622_3)
Sample type SRA
 
Source name total nuclei
Organism Caenorhabditis elegans
Characteristics age: adult
strain: JJ2289
cell type: whole organism
sample type: total nuclei
Extracted molecule genomic DNA
Extraction protocol INTACT (supplementary file INTACT_ChIP_protocol.rtf) but with MNase digestion for 5 minutes.
 
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina HiSeq 2000
 
Description MNase-protected DNA fragments in total nuclei
Illumina HiSeq 2000, Flow cell:v3.0, Software:HCS1.4.5/RTA 1.12.4
Data processing 1. We used Novoalign to map paired-end 25bp reads to release W220 of the C. elegans genomic sequence obtained from WormBase. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file Total_nuclei_2_20110622_3.bam) 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 Total_nuclei_2_20110622_3.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.
 
Submission date Oct 03, 2011
Last update date Jun 11, 2013
Contact name Jorja Henikoff
E-mail(s) jorja@fhcrc.org
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
 
Platform ID GPL13657
Series (1)
GSE31602 Tissue-specific nuclei purification from animal models for genome-wide expression and chromatin profiling.
Relations
BioSample SAMN02198011

Supplementary file Size Download File type/resource
GSM807109_INTACT_ChIP_protocol.txt.gz 1.2 Kb (ftp)(http) TXT
GSM807109_Solexa_library_protocol_GEO.pdf.gz 66.0 Kb (ftp)(http) PDF
GSM807109_Total_nuclei_2_20110622_3.bam 3.2 Gb (ftp)(http) BAM
GSM807109_Total_nuclei_2_20110622_3.bedgraph.gz 101.2 Mb (ftp)(http) BEDGRAPH
Raw data provided as supplementary file
Processed data provided as supplementary file
Processed data included within Sample table

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