|
| Status |
Public on Feb 25, 2016 |
| Title |
SP1173_WT ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
fission yeast cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: SP1173
genotype/variation: mat1M leu1-32 ade6-216 his2 ura4-D18
chip antibody: mouse monoclonal anti-V5/Pk1
chip antibody vendor: AbD Serotec, Kidlington, UK
chip antibody cat. #: MCA2324
chip antibody batch: #0911
|
| Growth protocol |
Cells were grown in liquid YEA media in a 32C shaker until exponential phase
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Exponentially growing cells were fixed in 3% paraformaldehyde, and chromatin was sheared into 500 to 700-bp fragments using a Misonix Sonicator 3000 (Qsonica, Newtown, CT). Chromatinassociated proteins were then immunoprecipitated using mouse monoclonal anti-V5/Pk SV5-Pk1 (AbD Serotec, Kidlington, UK) antibodies in combination with Protein G-coupled Dynabeads (Life Technologies, Carlsbad, CA).
Libraries were prepared from 3.1 ng of DNA using the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® with the NEBNext® Multiplex Oligos for Illumina® following manufacture’s protocol. Sequencing was perofromed by an Illumina HiSeq2000
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed Illumina CASAVA version 8
ChIp-seq reads were aligned to S.pombe genome (ASM294v1.18) using BWA version 0.6.2
Fragment shift length was estimated by using HOMER version 4.4
Treatment and control read density were normalized by using the ratio of total read number. The score of the peaks were determined by the subtraction of control read density from treatment read density and calculate 200bp window average.
Genome_build: ASM294v1.18 (download from ftp://ftp.ensemblgenomes.org/pub/fungi/release-18/fasta/schizosaccharomyces_pombe/dna/)
Supplementary_files_format_and_content: wig files. Score represent subraction of control read density from treatment read density
|
| |
|
| Submission date |
Oct 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Hideki Tanizawa |
| E-mail(s) |
hidekit@uoregon.edu
|
| Organization name |
University of Oregon
|
| Department |
Institute of Molecular Biology
|
| Street address |
1370 Franklin Blvd
|
| City |
Eugene |
| State/province |
OR |
| ZIP/Postal code |
97403 |
| Country |
USA |
| |
|
| Platform ID |
GPL13988 |
| Series (1) |
| GSE74487 |
Swi1/Timeless prevents repeat instability at fission yeast telomeres |
|
| Relations |
| BioSample |
SAMN04225792 |
| SRA |
SRX1397807 |
