|
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 |