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Sample GSM1921615 Query DataSets for GSM1921615
Status Public on Feb 25, 2016
Title SP1173_WT ChIP-seq
Sample type SRA
Source name fission yeast cells
Organism Schizosaccharomyces pombe
Characteristics strain: SP1173
genotype/variation: mat1M leu1-32 ade6-216 his2 ura4-D18
chip antibody: mouse monoclonal anti-V5/Pk1
chip antibody vendor: AbD Serotec, Kidlington, UK
chip antibody cat. #: MCA2324
chip antibody batch: #0911
Growth protocol Cells were grown in liquid YEA media in a 32C shaker until exponential phase
Extracted molecule genomic DNA
Extraction protocol Exponentially growing cells were fixed in 3% paraformaldehyde, and chromatin was sheared into 500 to 700-bp fragments using a Misonix Sonicator 3000 (Qsonica, Newtown, CT). Chromatinassociated proteins were then immunoprecipitated using mouse monoclonal anti-V5/Pk SV5-Pk1 (AbD Serotec, Kidlington, UK) antibodies in combination with Protein G-coupled Dynabeads (Life Technologies, Carlsbad, CA).
Libraries were prepared from 3.1 ng of DNA using the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® with the NEBNext® Multiplex Oligos for Illumina® following manufacture’s protocol. Sequencing was perofromed by an Illumina HiSeq2000
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Data processing Basecalls performed Illumina CASAVA version 8
ChIp-seq reads were aligned to S.pombe genome (ASM294v1.18) using BWA version 0.6.2
Fragment shift length was estimated by using HOMER version 4.4
Treatment and control read density were normalized by using the ratio of total read number. The score of the peaks were determined by the subtraction of control read density from treatment read density and calculate 200bp window average.
Genome_build: ASM294v1.18 (download from
Supplementary_files_format_and_content: wig files. Score represent subraction of control read density from treatment read density
Submission date Oct 29, 2015
Last update date May 15, 2019
Contact name Hideki Tanizawa
Organization name University of Oregon
Department Institute of Molecular Biology
Street address 1370 Franklin Blvd
City Eugene
State/province OR
ZIP/Postal code 97403
Country USA
Platform ID GPL13988
Series (1)
GSE74487 Swi1/Timeless prevents repeat instability at fission yeast telomeres
BioSample SAMN04225792
SRA SRX1397807

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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