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Sample GSM5715146 Query DataSets for GSM5715146
Status Public on Jan 17, 2022
Title Amanita_sir3-8-EcoGII_60min
Sample type SRA
 
Source name Amanita_sir3-8-EcoGII_60min
Organism Saccharomyces cerevisiae
Characteristics strain: JRY13134
condition: 60min after temperature switch from 37C to 25C; YPD
genotype: mat<delta>::KanMX, sir3-8-M.ECOGII-NatMX
Growth protocol Yeast were cultured at 30°C in YPD unless otherwise noted under "conditions" for each experiment/sample.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using the Zymo YeaStar genomic DNA Kit (Genesee Scientific, Cat #11-323). DNA was sheared to 15-25kb using a Covaris gTUBE and then concentrated and purified using 1X v/v SPRI Select beads (Beckman-Coulter B23317).
Oxford Nanopore Ligation Sequencing Kit (SQK-LSK109) with Native Barcode Expansion (EXP-NBD104).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model MinION
 
Description mat∆::KanMX, sir3-8-M.ECOGII-NatMX
Data processing Reads were basecalled and demultiplexed using guppy and guppy_barcoder. Read IDs were extracted using a custom python script and used to demultiplex fast5 files.
Reads were basecalled (including modified bases) and aligned to the SacCer3 genome (modified to include mat∆) using Megalodon and the all-context model (https://github.com/nanoporetech/rerio, res_dna_r941_min_modbases-all-context_v001.cfg) with the options --mod-motif “Y A 0”, --files_out “basecalls mod_mappings per_read_mods” and --read-ids-filename “barcodeXX_readIDs.txt” (the file that contained the extracted list of readIDs for a given barcode).
Data from the .db file were aggregated using Megalodon "megalodon_extras aggregate run".
Genome_build: SacCer3 (modified)
Supplementary_files_format_and_content: All experiments include a .bed file (bedMethyl format) aggregated using Megalodon (https://github.com/nanoporetech/megalodon "megalodon_extras aggregate run"). Experiments where single reads were analyzed include a .db file (SQLite database) generated using Megalodon. These .db files can be converted to .txt files using Megalodon "megalodon_extras per_read_text modified_bases".
 
Submission date Dec 03, 2021
Last update date Jan 19, 2022
Contact name Molly Brothers
E-mail(s) molly_brothers@berkeley.edu
Organization name University of California, Berkeley
Department Molecular and Cell Biology
Lab Rine Lab (440 Barker Hall)
Street address UC Berkeley 440 Barker Hall
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platform ID GPL25739
Series (2)
GSE190136 Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae [II]
GSE190137 Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae
Relations
BioSample SAMN23606366
SRA SRX13305449

Supplementary file Size Download File type/resource
GSM5715146_Amanita_sir3-8-EcoGII_60min_aggregate.6mA.bed.gz 81.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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