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Sample GSM2143339 Query DataSets for GSM2143339
Status Public on Jan 01, 2017
Title Ncrassa_hpo_BSseq
Sample type SRA
 
Source name mycelium
Organism Neurospora crassa
Characteristics growth medium: 1xVogels, 1.5% sucrose
growth time: 48 hrs.
genotype/variation: hpo
Growth protocol grown in 1xVogels medium + 1.5% sucrose for 48 hours on a rocking shaker at 32oC
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated using a protocol modified from (Oakley et al, 1987). Genomic DNA (50ng) was treated with bisulfite using the EZ DNA Methylation LightningTM kit (ZYMO Research) per the manufacturer's protocol.
Bisulfite-Seq Libraries were prepared for sequencing using the EpiGnomeTM Methyl-Seq Kit (Epicentre cat #EGMK91324) and EpiGnomeTM Index PCR Primers (Epicentre cat# EGIDX81312), the library was purified with Agencourt AMPure XP beads (Beckman Coulter), quantified using a Qubit HS Assay (Life Technologies), visualized on the Fragment AnalyzerTM (Advanced Analytical), and sequenced on a Illumina HiSeq 2000
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
 
Data processing The BRAT-BW software package (compbio.cs.ucr.edu/brat/; Harris et al, 2012) was used to prepare and map the reads to the N. crassa OR74A (annotation NC12) genome, which was converted to a four stranded reference genome to permit bisulfite mapping.
BRAT-BW acgt-count “-B” option cytosine-only files produced for the forward and reverse strand reads were merged.
The average 5mC level was determined for 500bp step-wise window size across the genome using the Methpipe program (http://smithlabresearch.org/software/methpipe/).
The resulting file was renamed with a “.igv” file extension to allow display on the Integrated Genome Viewer (IGV; www.broadinstitute.org/igv/)
Genome_build: NC12
Supplementary_files_format_and_content: .igv files displaying the % methylation over 500bp windows where a score of 0 is a DNA region that has no cytosine methylation and a score of 1.0 is DNA where all of the cytosines are methylated in the region. Values in between 0 and 1.0 represent partial methylation of a region.
 
Submission date May 05, 2016
Last update date May 15, 2019
Contact name Michael R Rountree
E-mail(s) mike.rountree@nzumbeinc.com
Organization name Nzumbe, Inc.
Street address 3429 NE Sandy Blvd. #330
City Portland
State/province OR
ZIP/Postal code 97232
Country USA
 
Platform ID GPL16164
Series (1)
GSE81129 Dual chromatin recognition by the histone deacetylase complex HCHC is required for proper DNA methylation in Neurospora crassa
Relations
BioSample SAMN04954988
SRA SRX1743293

Supplementary file Size Download File type/resource
GSM2143339_N4922_hpo_ROI500bp.igv.gz 1.4 Mb (ftp)(http) IGV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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