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Sample GSM5693584 Query DataSets for GSM5693584
Status Public on Nov 24, 2021
Title 210716_Solo_SIR3-EcoGII_m6A_DIP
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
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
BioSample SAMN23243312
SRA SRX13158386

Supplementary file Size Download File type/resource
GSM5693584_Solo_210716-JRY13027-IP_median_normalized.bedGraph.gz 64.2 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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