|
| Status |
Public on Nov 29, 2018 |
| Title |
H3T6rep1 |
| Sample type |
SRA |
| |
|
| Source name |
cell
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: 2352
chip antibody: H3
|
| Treatment protocol |
For Recombination Induced Tag Exchange experiment (RITE), cells were treated with 1 mM b-estradiol.
|
| Growth protocol |
Schizosaccharomyces pombe cell were grown in rich medium (1X YES).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were prepared using standard bead beating procedure, sonicated to achieve fragmements of 200-400bp andclarified by centrifugation at 17000g.
ChIP-Nexus libraries were prepared essentially as described in He et al., 2015, Briefly, protein G-dynabeads bound DNA-protein-complexes were affinity selected using specific antibodies . DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment and T4 polynucleotide kinase. A single 3'-A overhang was added using Klenow 3'-5' exo- polymerase. Adapters were ligated and blunted again by Klenow 3'-5' exo- polymerase to fill in the 5’ overhang first and then by T4 DNA polymerase to trim possible 3’ overhangs. Blunted DNA was then sequentially digested by lambda exonuclease and RecJf. Digested single strand DNA was then eluted, reverse cross-linked and phenol-chloroform purified. Fragments were then self-circularized by Circligase. An oligonucleotide was hybridized to circularized single DNA for subsequent BamHI digestion in order to linearize the DNA. This linearized single strand DNA was then PCR-amplified using adapter sequences and library was purified and size selected using Ampure XP beads. The sequencing libraries were sequenced following Illumina's work flow.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
ChIP-Nexus reads were aligned to ASM294v2.20 build using Bowtie2, trimmed first 15bp; Input data aligned to ASM294v2.20 build using Bowtie2;
ChIP-Nexus data were analysis using MACE; INPUT data were analysis using samtools and bedtools, Deeptools;
Genome_build: ASM294v2.20
Supplementary_files_format_and_content: Deeptools was used to generate 50bp slides window bw file.
|
| |
|
| Submission date |
Sep 13, 2018 |
| Last update date |
Nov 30, 2018 |
| Contact name |
Robin Allshire |
| E-mail(s) |
Robin.Allshire@ed.ac.uk
|
| Organization name |
The University of Edinburgh
|
| Lab |
Allshire Lab
|
| Street address |
Max Born Cresent
|
| City |
Edinburgh |
| State/province |
Midlothian |
| ZIP/Postal code |
EH9 3BF |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL23689 |
| Series (2) |
| GSE106494 |
Centromeric DNA destabilizes H3 nucleosomes to promote CENP-A deposition during the cell cycle |
| GSE119922 |
Centromeric DNA destabilizes H3 nucleosomes to promote CENP-A deposition during the cell cycle (part 3) |
|
| Relations |
| BioSample |
SAMN10056074 |
| SRA |
SRX4677066 |
