|
| Status |
Public on Jul 07, 2012 |
| Title |
hst4_Rpa1_IP |
| Sample type |
SRA |
| |
|
| Source name |
Haploid cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: h- leu1-32 ura4-D18 hst4D::kanMX rad11-TAP::kanR
chip antibody: IgG Sepharose 6 Fast Flow
antibody vendor/catalog#: GE Healthcare, 17-0969-02
|
| 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 |
SRX158050 |
| BioSample |
SAMN01086056 |
