|
| Status |
Public on Nov 24, 2021 |
| Title |
210114_Birthday_SIR3-EcoGII_m6A_input |
| Sample type |
SRA |
| |
|
| Source name |
Saccharomyces cerevisiae
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: JRY13027
ip antibody: anti-m6A antibody (Synaptic Systems 202-003, lot 2-109)
condition: Cycling
genotype: mat-delta::HphMX, SIR3-M.ECOGII-NatMX
|
| Treatment protocol |
For ChIP-seq experiments (Samples 1 and 2), cells were fixed in 1% formaldehyde for 15 minutes at 30°C and then quenched with 300mM glycine for 10min at 30°C.
|
| Growth protocol |
Yeast were cultured at 30°C in YPD except for the following: Samples 21 and 22 were grown at 25°C in YPD. Samples 23 and 24 were grown at 37°C in YPD.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed by mechanical disruption in a bead beater. Chromatin or DNA was fragmented using sonication. V5 immunoprecipitations were performed using anti-V5 antibody (Invitrogen R960-25). m6A immunoprecipitations were performed using anti-m6A antibody (Synaptic Systems 202-003). For ChIP-seq, DNA was purified with 1X v/v SPRI Select beads (Beckman-Coulter Beckman Coulter, B23317)
For ChIP-seq: NEB Ultra II library prep kit. For MeDIP-seq: Swift Biosciences Accel-NGS 1S Plus
ChIP-seq and MeDIP-seq
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina MiniSeq |
| |
|
| Data processing |
FASTQ generation with Illumina Casava v2.2
Raw reads were mapped to SacCer3 genome modified to include mat∆ using Bowtie2 with following options: --local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant
bedgraph files were normalized to the genome-wide median (median excluded subtelomeres, chromosome III, and rDNA)
Genome_build: SacCer3 (modified)
Supplementary_files_format_and_content: bedGraph (normalized to genome-wide median)
|
| |
|
| Submission date |
Nov 17, 2021 |
| Last update date |
Nov 24, 2021 |
| 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 |
GPL22715 |
| Series (2) |
| GSE189038 |
Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae [I] |
| GSE190137 |
Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae |
|
| Relations |
| BioSample |
SAMN23243307 |
| SRA |
SRX13158381 |
