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Sample GSM957313 Query DataSets for GSM957313
Status Public on Jul 07, 2012
Title hst4_Rad52_YFP_IP_1
Sample type SRA
 
Source name Haploid cells
Organism Schizosaccharomyces pombe
Characteristics genotype: h+ leu1-32 ura4-D18 hst4D::kanMX rad22-YFP-kanMX
chip antibody: GFP-Trap
antibody vendor/catalog#: ChromoTek, 101022001A
Growth protocol Cells used for ChIP assay were cultured in EMM (Edinburgh Minimal Medium) with necessary supplements at 30°C unless otherwise noted.
Extracted molecule genomic DNA
Extraction protocol ChIP DNA or input DNA was pre-denatured at 95°C and quenched on ice. The DNA was mixed with two pre-annealed adaptors added at final concentrations of 1.5 uM each. Adaptor 1 was composed of oligo A (5'-GCTCTTCCGATCXXXXCNNNNNN-3') and oligo B (5'-p-GXXXXGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-NH2-3'). XXXX in the oligo sequence denotes 4-nucleotide multiplex indexes. Adaptor 2 was composed of oligo C (5'-NNNNNNGTTCAGAGTTCTGCGACAGGAGAG-NH2-3') and oligo D (5'-CAAGCAGAAGACGGCATACGACCTCTCCTGTCGCAGAACTCTGAAC-3'). The ligation reaction was conducted using the Quick Ligation Kit (New England Biolabs) at 16°C overnight. The ligation product was then separated on a Low Range Ultra agarose gel (Bio-Rad). DNA in the 250-500-bp range was retrieved with the GFX PCR DNA and Gel Band Purification Kit (GE Healthcare). The gel-purified DNA was amplified by PCR using primers P1 (5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA-3') and P2 (5'-CAAGCAGAAGACGGCATACGA-3') for 25 cycles. The PCR product was processed by gel-based size selection, again retaining DNA in the 250-500-bp range. Equal amounts of DNA tagged with different multiplex indexes were mixed together and sequenced on an Illumina GA-II instrument using the sequence primer 5'-ACACTCTTTCCCTACACGACGCTCTTCCGATC-3'.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Data processing Basecalling by Illumina Casava software
Sequencing reads were trimmed for index sequence, and mapped to S. pombe reference genome using SOAP2 software, allowing only perfectly and uniquely-matched reads
Genome_build: S. pombe 972 strain
Supplementary_files_format_and_content: bed file. The values indicate the number of sequencing reads mapped to certain location.
 
Submission date Jul 06, 2012
Last update date May 15, 2019
Contact name Zhi-Xiong Zhou
E-mail(s) zhouzhixiong@nibs.ac.cn
Organization name National Institute of Biological Sciences, Beijing
Lab Dr. Li-Lin Du's lab
Street address No.7, ZGC Life Science Park
City Beijing
ZIP/Postal code 102206
Country China
 
Platform ID GPL9453
Series (1)
GSE39166 Strand-specific ChIP-seq profiling of Rad52 localization
Relations
SRA SRX158047
BioSample SAMN01086053

Supplementary file Size Download File type/resource
GSM957313_hst4_Rad52_YFP_IP_1.bed.gz 3.8 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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