|
| Status |
Public on Nov 29, 2018 |
| Title |
B324_T2_RNAPIIS2P |
| Sample type |
SRA |
| |
|
| Source name |
cell
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: B324
chip antibody: RNAPIIS2P
|
| Treatment protocol |
For Recombination Induced Tag Exchange experiment (RITE), cells were treated with 1 mM b-estradiol.
|
| Growth protocol |
Schizosaccharomyces pombe cell were gwon in rich medium (1X or 4X YES). Cell cycle synchronisation were performed using cdc25-22 temperature dependent block release.
|
| 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.
Libraries were prepared using standard Illumina pipeline. Briefly, DNA was end-repaired using NEB Quick blunting kit (E1201L). The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of NEXTflex adapters (Bioo Scientific) which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 13-15 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were selected using Ampure XP beads. The purified DNA was captured on an Illumina flow cell for cluster generation.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
ChIP-seq reads were aligned to ASM294v2.20 build using Bowtie2
Polymerase II ChIP-seq data were filtered pombe only reads;
Genome_build: ASM294v2.20
Supplementary_files_format_and_content: bigwig files were generated using bedtools and wigToBigWig from UCSC
|
| |
|
| Submission date |
Nov 03, 2017 |
| Last update date |
May 15, 2019 |
| 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 |
GPL17225 |
| Series (2) |
| GSE106492 |
Centromeric DNA destabilizes H3 nucleosomes to promote CENP-A deposition during the cell cycle (part 2) |
| GSE106494 |
Centromeric DNA destabilizes H3 nucleosomes to promote CENP-A deposition during the cell cycle |
|
| Relations |
| BioSample |
SAMN07975369 |
| SRA |
SRX3360059 |
