|
| Status |
Public on Nov 07, 2016 |
| Title |
57814sacCer3_KY404-pKB1140_5546_H2BK123ub_rtf1D_pHMD_rep4 |
| Sample type |
SRA |
| |
|
| Source name |
KY404-pKB1140
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
media: Sc-Trp
antibody: Cell Signaling 5546
antibody lot#: 1
genotype: MATa rtf1delta101::LEU2 his4-912delta lys2-128delta leu2delta1 ura3-52 trp1delta63 pKB1140(2micron, ADH1 NLS-3XHSV-HMD63-152, TRP1, KanR)
protocol: ChIP-exo
|
| Treatment protocol |
Cell were crosslink with 1% formaldehyde final concentration for 15 min.
|
| Growth protocol |
All yeast cells were grown to an OD600 of 0.6-0.8 at 30 °C following standard procedures in indicated media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-exo experiments were carried out essentially as described (Rhee and Pugh, 2012). Briefly, crosslinked cells were lysed, and chromatin pellets were isolated and then fragmented by sonication. Chromatin was then immunoprecipitated using antibody-conjugated magnetic beads, followed by DNA polishing, A-tailing, Illumina adaptor ligation (ExA2), and on beads digestion by lambda and recJ exonuclease. After elution of the single-stranded DNA, a primer was annealed to EXA2 and extended with phi29 DNA polymerase, then A-tailed. A second Illumina sequencing adaptor was ligated to exonuclease treated ends, and the products PCR-amplified and gel-purified.
ChIP-exo libraries were prepared for sequencing using standard Illumina protocols; Reference paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/
ChIP-exo-Seq
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Biological replicate 4 of 4, IP with anti-H2BK123ub antibody in rtf1D plasmid(HSV-HMD) strain
53101-02-57813-14sacCer3_KY404-pKB1140_5546_H2BK123ub_rtf1D_pHMD_comb_READ1_shift6.tab
|
| Data processing |
Basecalls performed using bcl2fastq ver 2.16 for NextSeq paired reads
ChIP-exo reads were aligned to Saccer3 genome assembly using bwa mem version 0.7.9a for paired reads. Read1 tags were shift 6 bp (to better reflect the crosslinking coordinates).
Genome_build: sacCer3/R64
Supplementary_files_format_and_content: tab files of shifted merge datasets used for mapping. Format: chr/index/forwardTag#/reverseTag#. The tab file of each combined dataset contains the coordinates of the shifted (6bp in the 3' direction) exo digested end (5') corresponding to the Read 1 of the sequencer.
|
| |
|
| Submission date |
Jun 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Alain Roger Bataille |
| E-mail(s) |
[email protected]
|
| Organization name |
Penn State University
|
| Department |
BMB
|
| Lab |
Dr B. Frank Pugh
|
| Street address |
453 North Frear
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL19756 |
| Series (1) |
| GSE83348 |
The Histone Modification Domain of Paf1 Complex Subunit Rtf1 Promotes H2B Ubiquitylation Through a Direct Interaction with the Ubiquitin Conjugase Rad6 |
|
| Relations |
| BioSample |
SAMN05247019 |
| SRA |
SRX1844595 |
