|
Status |
Public on Apr 26, 2021 |
Title |
Activation screen, Library A+B, INPUT |
Sample type |
SRA |
|
|
Source name |
Library A+B, INPUT
|
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 |
SAMN18836481 |
SRA |
SRX10660763 |