|
| Status |
Public on Jul 03, 2018 |
| Title |
History-dependence BAR-Seq [6] |
| Sample type |
SRA |
| |
|
| Source name |
Amplified barcodes from pooled Yeast Deletion collection
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
background strain: BY4730, NatR:MAL63::MAL13, MAL12:yEcitrine:LEU2, MAL11:mCherry:URA3
condition: 4h in glucose
|
| Growth protocol |
Yeast deletion collection pooled together and grown in YP-glu5% or YP-mal10%
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using a Zymolyase-based protocol, and the genomic DNA extracts were equalized based on the cell density of the samples. BAR-seq; PMID: 24192834
PCR barcode amplification of the UP and DN barcodes was done using primer sets (UP-tag: U1 and p69; DN-tag: D1 and D2) that generate respectively 168bp and 190bp fragments containing these barcodes at one of their ends. Ex-Taq polymerase (TaKaRa) was used using standard cycling conditions, including 30s of elongation time and an annealing temperature of 55°C. A limited number of amplification cycles (16) was done to avoid issues associated with over- amplification.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
sample name:
6
DNA barcode of deleted cassette
|
| Data processing |
Library strategy: BAR-seq
Blast the barcodes against the sequencing reads and get the number of counts allowing for 2 mismatches and 3 gaps
Genome_build: not-applicable
Supplementary_files_format_and_content: CSV format with the count of barcodes of each gene deletion in each condition. The results for the up-tag and down-tag of the deletion cassette are separated. Please see the FASTA files on the series record for barcode sequences and the "Readme_barcodePositions.pdf" file for explanation of the Yeast Deletion Collection used in this study.
|
| |
|
| Submission date |
Jul 02, 2018 |
| Last update date |
Jul 05, 2018 |
| Contact name |
Abbas Jariani |
| E-mail(s) |
jariani.abbas@gmail.com
|
| Phone |
+3168
|
| Organization name |
KU Leuven - VIB
|
| Department |
KU Leuven - VIB Centre for Microbiology
|
| Street address |
Gaston Geenslaan 1, box 2471
|
| City |
Leuven |
| ZIP/Postal code |
3001 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL19756 |
| Series (1) |
| GSE116505 |
BAR-Seq to study history-dependent behavior |
|
| Relations |
| BioSample |
SAMN09532916 |
| SRA |
SRX4330676 |
