|
| Status |
Public on Jan 17, 2022 |
| Title |
Russula_sir3-8-EcoGII_60min |
| Sample type |
SRA |
| |
|
| Source name |
Russula_sir3-8-EcoGII_60min
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: JRY13114
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 |
SAMN23606341 |
| SRA |
SRX13305455 |
