|
| Status |
Public on Jul 10, 2019 |
| Title |
WTCHG_543859_213140: GC rich Cnp1 before deletion |
| Sample type |
SRA |
| |
|
| Source name |
fission yeast cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: Nott860
tissue: fission yeast cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Material was quantified using Qubit (Invitrogen) and the size profile analysed on the 2200 or 4200 TapeStation (Agilent, dsDNA HS Assay). Input material was normalised to 5 ng or maximum available prior to library preparation. Automated library preparation was performed using the Apollo prep system (Wafergen, PrepX ILMN 32i, 96 sample kit) and standard Illumina multiplexing adapters following manufacturer’s protocol up to pre-PCR amplification. Libraries were PCR amplified (18 cycles) on a Tetrad (Bio-Rad) using the NEBNext High-Fidelity 2X PCR Master Mix (NEB) and using in-house unique dual indexing primers (based on DOI: 10.1186/1472-6750-13-104). Individual libraries were normalised using Qubit, and the size profile was analysed on the 2200 or 4200 TapeStation. Individual libraries were normalised and pooled together accordingly. The pooled library was diluted to ~10 nM for storage. The 10 nM library was denatured and further diluted prior to loading on the sequencer. Paired end sequencing was performed using a HiSeq4000 75bp platform (Illumina, HiSeq 3000/4000 PE Cluster Kit and 150 cycle SBS Kit), generating a raw read count of >8 million reads per sample.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The software Burrows-Wheeler Aligner (BWA) (v0.7.15-r1142-dirty) was used for all the alignments using algorithm “mem” with standard parameters.
Samtools (v1.3.1) was used to select the reads mapped in correct orientation and within insert size.
Coverage vectors were created for using the R package Bioconductor (v3.6).
Coverage plots were created in R (http://www.r-project.org) and were smoothed using the default running medians scatter plot smoothing in R.
Supplementary_files_format_and_content: no processed data because tracks are not applicable to the engineered strains
|
| |
|
| Submission date |
Feb 13, 2019 |
| Last update date |
Jul 10, 2019 |
| Contact name |
William Brown |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Nottingham
|
| Department |
School of Life Sciences
|
| Street address |
Queens Medical Centre
|
| City |
Nottingham |
| ZIP/Postal code |
NG7 2UH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL22682 |
| Series (1) |
| GSE126511 |
Budding yeast centromeric DNA and A+T rich bacterial DNA can function as centromeres in the fission yeast Schizosaccharomyces pombe |
|
| Relations |
| BioSample |
SAMN10925006 |
| SRA |
SRX5372052 |
