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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
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 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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