|
| Status |
Public on Aug 05, 2018 |
| Title |
subsequences_offtarget_2 |
| Sample type |
SRA |
| |
|
| Source name |
Cells
|
| Organism |
Saccharomyces cerevisiae x Saccharomyces uvarum |
| Characteristics |
growth conditions: saturated in YPD
restriction enzyme: DpnII
|
| Treatment protocol |
Cells were crosslinked by addition of 37% formaldehyde to a 1% final concentration, for 20 minutes at room temperature, and then quenched by addition of 2.5M glycine, incubation for 5 minutes, and a TBS (Tris-buffered saline) wash.
|
| Growth protocol |
Cells were grown overnight, shaking at 30C in YPD media (1% yeast extract, 2% peptone, 2% dextrose).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed using glass beads and chromatin was extracted, digested using restriction enzyme, and ligated. Crosslinks were reversed and DNA was purified by phenol/chloroform extraction.
DNA was amplified with primers containing sequencing and flowcell adapter sequences.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
HAS1pr-TDA1pr.fa
|
| Data processing |
Library strategy: subsequences cis MAP-C
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were trimmed of adapter sequences and merged using PEAR
Reads were mapped were trimmed of the first 4 bp (corresponding to a randomized region for Illumina clustering purposes) to the S. cerevisiae HAS1pr-TDA1pr region, or the mutagenized subset thereof using Bowtie2. For subsequences, read coverage was calculated using bedtools.
Genome_build: Saccharomyces cerevisiae R64.2.1 from SGD
Supplementary_files_format_and_content: tab-delimited text files ending in "cov.txt" include the raw read coverage at each position within the HAS1pr-TDA1pr region. FASTA files ending in ".fa" include the names and sequences of the regions used as references for alignment.
|
| |
|
| Submission date |
Aug 03, 2018 |
| Last update date |
Feb 15, 2019 |
| Contact name |
Seungsoo Kim |
| Organization name |
Stanford University
|
| Department |
Chemical and Systems Biology
|
| Lab |
Joanna Wysocka
|
| Street address |
265 Campus Dr
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL25423 |
| Series (1) |
| GSE118118 |
A combination of transcription factors mediates inducible interchromosomal contacts |
|
| Relations |
| BioSample |
SAMN09765440 |
| SRA |
SRX4507091 |
