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Sample GSM1634684 Query DataSets for GSM1634684
Status Public on Oct 18, 2015
Title leo1_H3K9me2 rep1
Sample type SRA
 
Source name leo1_H3K9me2
Organism Schizosaccharomyces pombe
Characteristics strain: Hu2689
genotype: leo1::kan
chip antibody: H3K9me2 (Abcam ab1220)
Growth protocol Liquid cultures were grown in YES media shaking at 180 rpm at 30°C.
Extracted molecule genomic DNA
Extraction protocol Immunoprecipitation was done using indicated antibody from chromatin extracts prepared from mid-logarithmic phase cells. Briefly, cells were fixed in 1% formaldehyde for 30 minutes, quenched with 125 mM glycine, and washed twice in PBS. Cells were resuspended in lysis buffer (0.1% SDS, 50 mM Hepes-KOH, 1 % Triton X-100, 0.1 % sodium deoxucholate, 1 mM EDTA and 150 mM NaCl) and lysed with glass beads in a FastPrep homogenizer. The lysate was sonicated and soluble chromatin fragments with an average size of 300 bp were collected. Chromatin was immunoprecipitated with indicated antibody and protein A magnetic beads overnight. The beads were washed.
With the immunoprecipitate still on the beads, the DNA was polished, A-tailed, and ligated to an Illumina sequencing library adaptor. Digestion lambda exonuclease (final concentration 2.5U/reaction) removed nucleotides from 5′ ends of double-stranded DNA until blocked by the formaldehyde induced protein-DNA crosslink. The crosslinks were reversed (4h at 65°C) and DNA was eluted from the beads. The single-stranded DNA was subsequently made double-stranded by primer annealing and extension. A second sequencing adaptor was ligated. Using indexing primers, the fragments were PCR amplified and gel purified (Qiagen MinElute). Samples were quantified on using Qubit (HS dsDNA).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description ChIP-exo
Data processing Read alignment using Bowtie 2 (default parameters)
SAM files loaded into Podbat 0.6.0 (www.podbat.org) with options "first base only", "resolution"=25, "strand-specific" unchecked, MAPQ>0
Normalized to total # reads
Exported to wig.
Genome_build: ASM294v2
Supplementary_files_format_and_content: wig format, variable step
 
Submission date Mar 16, 2015
Last update date May 15, 2019
Contact name Karl Ekwall
E-mail(s) karl.ekwall@ki.se
Phone +46 8 6089133
Organization name Karolinska Inst
Street address Alfred Nobels Alle 7
City Stockholm
ZIP/Postal code S-141 89
Country Sweden
 
Platform ID GPL13988
Series (2)
GSE66939 Paf1 complex factors, Leo1 and Paf1, promote local histone turnover to modulate chromatin states in fission yeast [ChIP-exo]
GSE66941 Paf1 complex factors, Leo1 and Paf1, promote local histone turnover to modulate chromatin states in fission yeast
Relations
BioSample SAMN03418357
SRA SRX957556

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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