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Sample GSM1051304 Query DataSets for GSM1051304
Status Public on Jul 20, 2013
Title clr4D_H3K9me2_ChIPSEQ_rep1
Sample type SRA
 
Source name clr4D H3K9me2 ChIPSEQ
Organism Schizosaccharomyces pombe
Characteristics genotype: clr4D
chip antibody: H3K9me2
chip antibody manufacturer: WAKO
chip antibody catalog #: MABI0307
chip antibody lot #: 302-32369
Growth protocol S.pombe strains were grown in YES media. ~150x10^7 cells were harvested from o/n cultures and processed for ChIP
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated S. pombe cells and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were generated using an Illumina-based protocol using custom reagents and barcoded adapters. Briefly, immunoprecipitated DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA fragments were size selected to remove excess adapters and adapter modified DNA fragments were enriched by PCR amplification with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified ChIP-seq libraries thus generated were validated and subsequently captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 system following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description AGAAGCT
Data processing All samples were barcoded at the 3'end of the 5'adapter using a hamming distance two code with a 3' CT (GTGCGCT, GCCACCT, AGAAGCT, ATCTTCT, TGCCACT, CACGGCT, CGGTCCT, CCACTCT) and sequenced (with other samples) in two lanes of an HiSeq 2000 instrument. Individual reads were assigned to their sample based on the first 7 nucleotides containing the barcode. The 3' adapter was removed by aligning it to the read allowing one or two mismatches in prefix alignments of at least 7 or 10 bases respectively. Low complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). All the reads that were shorter than 14 nucleotides were removed.
Genome_build: Initial identification of elements is based on the features described in the GFF file “pombe_09052011.gff” (downloaded from ftp://ftp.sanger.ac.uk/pub/yeast/pombe/GFF).
Supplementary_files_format_and_content: wig file for multiple tracks
 
Submission date Dec 11, 2012
Last update date May 15, 2019
Contact name Tim Roloff
E-mail(s) tim.roloff@fmi.ch
Organization name FMI
Department Functional Genomics
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
 
Platform ID GPL13988
Series (2)
GSE42848 Genome wide map of heterochromatin state in fission yeast Schizosaccharomyces pombe
GSE42850 Heterochromatin state in fission yeast Schizosaccharomyces pombe
Relations
SRA SRX209509
BioSample SAMN01830779

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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