|
| Status |
Public on Dec 27, 2023 |
| Title |
ISW2_2 |
| Sample type |
SRA |
| |
|
| Source name |
yeast cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell lines: Y0105/Y0106/Y0102/Y0107
cell type: yeast cells
genotype: Y0105: MATa; ura3delta0; leu2delta0; his3delta1; met15delta0; bar1::kanMX4; RS_LEXA_NS- 3_ARS305_NS+3_RS; Chr I 212kb::LEU2 pTEF2-LEXATAP pGAL1-10 RecR ;isw2delta::ura3
genotype: Y0106: MATa; ura3delta0; leu2delta0; his3delta1; met15delta0; bar1::kanMX4; RS_LEXA_NS- 3_ARS316_NS+3_RS; Chr I 212kb::LEU2 pTEF2-LEXATAP pGAL1-10 RecR;isw2delta::ura3
genotype: Y0102: MATa; ura3delta0; leu2delta0; his3delta1; met15delta0; bar1::kanMX4;RS_LEXA_NS- 3_ARS315_NS+3_RS; Chr I 212kb::LEU2 pTEF2-LEXATAP pGAL1-10 RecR ; isw2delta::ura3
genotype: Y0107: MATa; ura3delta0; leu2delta0; his3delta1; met15delta0; bar1::kanMX4;RS_LEXA_NS- 3_ARS313_NS+3_RS; Chr I 212kb::LEU2 pTEF2-LEXATAP pGAL1-10 RecR;isw2delta::ura3
|
| Growth protocol |
Logarithmic yeast cells were grown in YPR medium and arrested with alpha-factor together with addition of 2% galactose to induce site-specific recombination of native replication origin chromatin domains. Cells were harvested and frozed for subsequent affinity purification.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell pellets were lysed with dry ice in a commercial coffee grinder and chromatin domains affinity-purified as described in the manuscript. The purified chromatin circles were then treated with the M.CviPI/M.SssI (GpC/CpG-5-methyl-Cytosine-specific) and EcoGII (methyl-6-Adenine-specific) DNA methyltransferases. Methylated DNA was then isolated using Phenol-chloroform extraction. EcoGII (methyl-6-Adenine-specific) DNA methyltransferases,
MinIONTM Seqencing Library Preparation (Oxford Nanopore Sequencing)
Nanopore long-read sequencing for direct detection of methylated bases
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
MinION |
| |
|
| Data processing |
Base- and modified basecalling were performed with megalodon (v2.3.3) and guppy (v5.0.11) using the res_dna_r941_min_modbases-all-context_v001 model and default parameters.
ARS sequences derived from genome build/assembly Saccharomyces_cerevisisae.R64-1-1 targeted for affinity purification, an in vitro assembled nucleosomal array of 12x601 sequences and a spike-in naked plasmid DNA added in the experiments served as spike-in controls to normalize for methylation efficiencies.
Assembly: Saccharomyces_cerevisiae.R64-1-1
Supplementary files format and content: comma separated files that contain binary information about methylation
|
| |
|
| Submission date |
Dec 12, 2022 |
| Last update date |
Dec 27, 2023 |
| Contact name |
Stephan Hamperl |
| E-mail(s) |
stephan.hamperl@helmholtz-munich.de
|
| Phone |
+4989318746492
|
| Organization name |
Helmholtz-Zentrum Munich
|
| Department |
Institute of Epigenetics and Stem Cells
|
| Lab |
Hamperl
|
| Street address |
Feodor-Lynen-Strasse 21
|
| City |
Munich |
| State/province |
Bayern |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL25739 |
| Series (1) |
| GSE220757 |
Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency |
|
| Relations |
| BioSample |
SAMN32190285 |
| SRA |
SRX18670377 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6813784_ARS305_disw2_rep2_780READS_noNA.csv.gz |
68.1 Kb |
(ftp)(http) |
CSV |
| GSM6813784_ARS313_disw2_rep2_780READS_noNA.csv.gz |
60.3 Kb |
(ftp)(http) |
CSV |
| GSM6813784_ARS315_disw2_rep2_780READS_noNA.csv.gz |
78.9 Kb |
(ftp)(http) |
CSV |
| GSM6813784_ARS316_disw2_rep2_780READS_noNA.csv.gz |
78.0 Kb |
(ftp)(http) |
CSV |
| GSM6813784_array_disw2_rep2_780READS_noNA_cleaned.csv.gz |
230.7 Kb |
(ftp)(http) |
CSV |
| GSM6813784_disw2_all_meth_REP2_ARS305_minus.txt.gz |
66.5 Kb |
(ftp)(http) |
TXT |
| GSM6813784_mat_Megalodon_20220221_disw2_all_meth_REP2_ARS313_end_LexA_minus.txt.gz |
60.6 Kb |
(ftp)(http) |
TXT |
| GSM6813784_mat_Megalodon_20220221_disw2_all_meth_REP2_ARS315_starting_LexA_minus.txt.gz |
82.3 Kb |
(ftp)(http) |
TXT |
| GSM6813784_mat_Megalodon_20220221_disw2_all_meth_REP2_ARS316_end_LexA_minus.txt.gz |
78.3 Kb |
(ftp)(http) |
TXT |
| GSM6813784_mat_Megalodon_20220221_disw2_all_meth_REP2_in_vitro_nucl_array_minus.txt.gz |
98.1 Kb |
(ftp)(http) |
TXT |
| GSM6813784_mat_Megalodon_20220221_disw2_all_meth_REP2_naked_plasmid_minus.txt.gz |
522.5 Kb |
(ftp)(http) |
TXT |
| GSM6813784_naked_plasmid_disw2_rep2_clean_780_reads.csv.gz |
978.6 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
