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| Status |
Public on Mar 21, 2024 |
| Title |
wild type live cells, 60 m SM, replicate 1 |
| Sample type |
SRA |
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| Source name |
Not Applicable
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
tissue: Not Applicable
strain: YHP827
genotype: MATa ade2-1 can1-100 leu2-3,112 trp1-1 ura3-1 ho::TIR1-MSssI-degron-3HA-KanMX
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Replicate 1 and YDC111 DNA samples were purified from yeast cells using New England Biolabs Monarch High Molecular Weight DNA kit. Replicate 2 DNA samples were purified yeast cells by extracting proteins three times with SDS, washing out the SDS, then removing the cell wall using lytic enzyme. The DNA was purified by chloroform extraction and isopropanol precipitation and a 70% ethanol wash. The DNA was further purified using Beckman-Coulter Ampure beads at a 0.4:1 volume ratio.
Libraries were prepared following Oxford Nanopore Technologies protocols. Replicate 1 and YDC111 samples were prepared with SQK-LSK110 kit protocols, while Replicate 2 samples were prepared with SQK-LSK109 and Native Barcoding (EXP-NBD104) kit protocols.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
MinION |
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| Data processing |
Basecalling with Guppy version 6.3.8 (or newer)
Indexing of basecalled reads with Nanopolish version 0.14.0
Alignment of basecalled reads to yeast genome with Minimap version 2.24 and sorting/indexing of aligned reads with samtools version 1.17
Likelihood of methylation at CpGs scored by Nanopolish v0.14.0: 'fmeth'.
The data were processed to obtain a wig file to display the fraction of C methylated at each CG in the genome (or unresolved group of CG sites), 'fmeth', for each sample.
Assembly: sacCer3
Supplementary files format and content: wig files containing fmeth values for each CG or group of CG sites in the yeast genome for display in IGV
Library strategy: whole genome sequencing
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| Submission date |
Apr 21, 2023 |
| Last update date |
Mar 21, 2024 |
| Contact name |
David Johannes Clark |
| E-mail(s) |
clarkda@mail.nih.gov
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| Phone |
3014966966
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| Organization name |
NICHD, NIH
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| Department |
DDB
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| Lab |
SCGE
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| Street address |
6 Center Drive Bldg 6A Rm 2A02
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL25739 |
| Series (2) |
| GSE230306 |
The yeast genome is globally accessible in living cells [OxfordNanopore] |
| GSE230309 |
The yeast genome is globally accessible in living cells |
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| Relations |
| BioSample |
SAMN34337149 |
| SRA |
SRX20077541 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7212153_fmeth_MSssI_Rep1_60m.wig.gz |
1.0 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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