|
| Status |
Public on Apr 26, 2021 |
| Title |
Activation screen, Library D+E, Bin 5 |
| Sample type |
SRA |
| |
|
| Source name |
Library D+E, Bin 5
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: strain BY4711
|
| Treatment protocol |
overnight cultures were diluted to OD600 of 0.4 in SC-Trp-NAT-G418 with 10 nM beta-estradiol and grown for 4 hours at 30C before sorting on a BD Influx Cell Sorter
|
| Growth protocol |
S. cerevisiae strain BY4711 (ATCC 200873) was cultured in SC medium lacking tryptophan (SC-Trp)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sorted cells were grown overnight and then pelleted. Pellets were treated with lyticase and then plasmid DNA was extracted using a Qiagen Miniprep kit.
The region of the plasmid encoding the variable protein fragment was PCR-amplified for 11-20 cycles (based on the OD600 of the culture) using Phusion polymerase with PCR primers that added flanking sequences corresponding to the standard Illumina sequencing primers. After a column cleanup, a second PCR was performed with primers that added sample-specific barcodes and the P5 and P7 sequences for Illumina sequencing.
OTHER:sequncing of designed plasmid library
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
Plasmid library DNA
|
| Data processing |
cutadapt 1.18 was used to discard reads without matching paired-end sublibrary sequencing primers and trim the primers in reads with matching primers
bwa-mem 0.7.17-r1188 was used to perform a first-pass alignment of reads to the DNA fragment library
Imperfectly mapped read pairs (i.e., those without paired read SAM flags of 99 and 147) were re-mapped to the library sequence with minimal edit distance
Supplementary_files_format_and_content: Excel file containing counts of reads aligned to each protein fragment
|
| |
|
| Submission date |
Apr 22, 2021 |
| Last update date |
Apr 26, 2021 |
| Contact name |
Adrian L Sanborn |
| E-mail(s) |
a@adriansanborn.com
|
| Organization name |
Stanford University
|
| Street address |
299 Campus Drive West
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL26302 |
| Series (2) |
| GSE173149 |
Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator (Activation) |
| GSE173156 |
Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator |
|
| Relations |
| BioSample |
SAMN18836476 |
| SRA |
SRX10660768 |
