|
| Status |
Public on Mar 22, 2015 |
| Title |
WT_Ncrassa_BSseq |
| Sample type |
SRA |
| |
|
| Source name |
N3752 WT Ncrassa (Selker)
|
| Organism |
Neurospora crassa |
| Characteristics |
strain: wildtype
time point in light cycle: 0
growth medium: 1xVogels, 1.5% sucrose (minimum)
bisulfite treated: bisulfite
|
| Growth protocol |
grown under standard dark cycle in 1xVogels medium + 1.5% sucrose (minimum medium) or minimum medium supplemented with histidine (0.5mg/mL [final]) for 48 hours on 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.
Libraries were prepared for sequencing with the EpiGnomeTM Methyl-Seq Kit (Epicentre cat #EGMK91324) and EpiGnomeTM Index PCR Primers (Epicentre cat# EGIDX81312) per the manufacturer's protocol, purified with Agencourt AMPure XP beads (Beckman Coulter) per the manufacturer's protocol, Qubit HS Assay quantified (Life Technologies) per the manufacturer's protocol, visualized on the Fragment AnalyzerTM (Advanced Analytical) per the manufacturer's protocol, 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.
A python script (bidensity) was written to calculate the average 5mC level over a 500bp sliding window across the genome, producing a .wig file
.wig files were displayed on IGV (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011)
Genome_build: Ncrassa version12
Supplementary_files_format_and_content: .wig files show the ratio (0-1.0; 0 is DNA that is not cytosine methylated, 1.0 is DNA where all of the cytosines are methylated) of methylated cytosines to unmethylated cytosines as peaks of cytosine methylation enrichment
|
| |
|
| Submission date |
Sep 05, 2014 |
| Last update date |
Feb 11, 2021 |
| Contact name |
Andrew David Klocko |
| E-mail(s) |
aklocko@uccs.edu
|
| Phone |
719-255-3255
|
| Organization name |
University of Colorado Colorado Springs
|
| Department |
Chemistry and Biochemistry
|
| Lab |
Klocko
|
| Street address |
278 Centennial Hall, 1420 Austin Bluffs Pkwy
|
| City |
Colorado Springs |
| State/province |
Colorado |
| ZIP/Postal code |
80918 |
| Country |
USA |
| |
|
| Platform ID |
GPL16164 |
| Series (2) |
| GSE61174 |
Bisulfite-seq from Neurospora crassa a wild type (WT) strain grown in minimum medium, a dim-3 strain grown in minimum medium, and a dim-3 strain grown with supplemented histidine |
| GSE61175 |
Neurospora importin alpha compromises H3K9me3 and cytosine methylation levels through inappropriate localization of the heterochromatin machinery |
|
| Relations |
| Alternative to |
GSM5077387 |
| BioSample |
SAMN03020661 |
| SRA |
SRX693079 |
