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Sample GSM590215 Query DataSets for GSM590215
Status Public on Sep 02, 2010
Title nakedDNA_MNase_seq
Sample type SRA
 
Source name naked DNA digested with Mnase
Organism Caenorhabditis elegans
Characteristics strain: N2
developmental stage: --
Treatment protocol No treatment
Growth protocol Genomic DNA from N2 was prepared. DNA was cut with MNase to fragments less than 500 bp.
Extracted molecule genomic DNA
Extraction protocol MNase digested 50 ng DNA was incubated with End Repair Enzyme mix (NEB Klenow, T4 DNA polymerase and T4 PNK) to ensure blunt ends and then with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3’ ends. The DNA fragments were ligated with single-end adaptor (Illumina) and then amplified by PCR with single end primers. The amplicon was loaded into an agarose gel, and mononucleosome length DNA was recovered from the gel. For a detailed protocol see http://www.modencode.org/ protocol:Solexa Library Preparation:JL:SE1
 
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina Genome Analyzer II
 
Description sequencing of naked DNA digested with Mnase
Data processing Raw coverage tracks: The sequencing was done using Illumina paired end reads technology. All lanes of each replicate were combined and mapped together. The two single reads of each pair were mapped independently to WS170 genome, using a proprietary software (SeqHit) allowing a single mismatch and no gaps. The hits of the non unique reads were extended to a nucleosomes length and their union defined the non unique regions. The pairs of mapped reads that define a valid (up to 200 basepairs length) and unique regions are collected. The raw coverage of a basepair is caluclated by summing up the number of unique reads covering it. Zero value is assigned to unique basepairs that were covered by none.
 
Submission date Sep 02, 2010
Last update date May 15, 2019
Contact name Jason D Lieb
E-mail(s) jlieb@bio.unc.edu
Phone 919-843-3228
Organization name University of North Carolina at Chapel Hill
Department Biology
Lab Jason Lieb
Street address 408 Fordham Hall, CB# 3280
City Chapel Hill
State/province NC
ZIP/Postal code 27599-3280
Country USA
 
Platform ID GPL9269
Series (1)
GSE20136 Genome-wide nucleosome occupancy profiling by high throughput sequencing, and microarray analysis of RNA abundance
Relations
SRA SRX026403
BioSample SAMN00110504
Named Annotation GSM590215_NakedDNA_Rep1_RawCoverage.wig.gz

Supplementary file Size Download File type/resource
GSM590215_NakedDNA_Rep1_RawCoverage.wig.gz 26.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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