|
| Status |
Public on Aug 05, 2018 |
| Title |
fixed-locus_ko_genomic_1 |
| Sample type |
SRA |
| |
|
| Source name |
Cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
growth conditions: saturated in YPD
restriction enzyme: EcoRI-HF
|
| 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 NextSeq 500 |
| |
|
| Description |
fixed-locus_ko_barcodes.fa
fixed-locus_ko_associations.txt
|
| Data processing |
Library strategy: fixed-locus trans MAP-C
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were trimmed to a fixed length of 25 bp and mapped to the set of possible barcodes using Bowtie2. Barcodes were associated with gene knockouts based on programmed barcode associations.
Genome_build: Barcode file fixed-locus_ko_barcodes.fa
Supplementary_files_format_and_content: tab-delimited text files ending in "counts.txt" include an identifier for each barcoded construct, the systematic name of the gene knockout, and the number of reads containing each barcode. FASTA files ending in ".fa" contain the possible barcodes used for mapping. tab-delimited text files ending in "associations.txt" include the gene knockout (including "r" for replicates) and the systematic gene name.
|
| |
|
| 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 |
GPL19756 |
| Series (1) |
| GSE118118 |
A combination of transcription factors mediates inducible interchromosomal contacts |
|
| Relations |
| BioSample |
SAMN09765418 |
| SRA |
SRX4507114 |
