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Sample GSM5724745 Query DataSets for GSM5724745
Status Public on Dec 17, 2021
Title Sample 1: Src_Variant_Library
Sample type SRA
 
Source name Synthetic sequence
Organism Escherichia coli
Characteristics strain: Top10
treatment: NA
treatment concentration: NA
molecule: Plasmid DNA
Treatment protocol S. cerevisiae harboring Src variant library were grown in 2% galactose containing media to induce Src expression and in varying concentrations of indicated Src kinase inhibitor. Library was grown and 4 OD unit timepoints were harvested throughout growth. The indicated concentration of Src inhibitor was added at the same time Src kinase expression was induced by galactose.
Growth protocol TOP10 E.coli were grown in LB supplemented with 100 ug/mL Ampicillin. BY4741 ∆PDR5 or BY4741 Green Monster S. cerevisiae were grown in C-Leu media supplemented with 2% galactose.
Extracted molecule other
Extraction protocol Harvested cells (4 OD units worth) at each sampled time point were pelleted and stored at -20ºC. Plasmid DNA was extracted using Zymogen Yeast Miniprep Kit I following supplied protocol.
Extracted barcodes were amplifed and sample indices appended using 2x KAPA2G Robust HotStart ReadyMix with Thermocycler conditions of: Initial denaturation at 95ºC for 3 min, followed by 17 cycles of 95ºC for 15s, 60ºC for 15s, and 72ºC for 15s. Amplicons were quantified using KAPA Library Quantification Kit.
DNA amplicon sequencing using custom primers
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
 
Description Library and barcode sequencing from DNA
Src_Barcode_Map.txt
Data processing Sample 1 was sequenced on MiSeq (Illumina). Samples 2-5 were sequenced on NextSeq 500 (Illumina).
All reads were processed using bcl2fastq v.2.16 and ea-utils v.1.1.2-537.
Sample 1: Custom scripts were used to process these reads. R2 files were trimmed to 230bp.
Samples 2-5: Functional scores were calculated using Enrich2 v1.2 software and Src_Barcode_Map.txt.
Genome_build: NA
Supplementary_files_format_and_content: Src_Barcode_Map.txt provides the linkage between the barcode sequence (first column) and the full length variant sequence of Src's catalytic domain (second column). This document was generated through the following steps: 1)Custom subassembly scripts to link barcode sequence with full length catalytic domain sequence. 2) Custom subassembly filtering script for high quality reads. 3) Filtering out WT barcodes with aberrant activity score using 2x Std. Dev. of WT barcode mean activity score. 4) Spike in of 6 barcode sequences of control Src variants (3 each for K298M and T341I).
Supplementary_files_format_and_content: Src_Das_25_Score.csv, Src_DAS_100_Score.csv, Src_1_8000_Score.csv, Src_2_2000_Score.csv, and Src_4_800_Score.csv are the output of Enrich2 v1.2. The inputs for Enrich2 v1.2 were the corresponding "Raw Files" (Input, A, B, and C) that share the same Src Inhibitor and concentration. Variants are denoted by their amino acid level changes and each has a calculated functional score from Enrich2.
 
Submission date Dec 08, 2021
Last update date Dec 17, 2021
Contact name Douglas Fowler
E-mail(s) dfowler@uw.edu
Organization name University of Washington
Department Genome Sciences
Lab Fowler
Street address 3720 15th Ave NE, Foege Building, S041
City Seattle
State/province WA
ZIP/Postal code 98195
Country USA
 
Platform ID GPL16085
Series (1)
GSE190495 Drug resistance profiling of thousands of Src kinase mutants uncovers a regulatory network that couples autoinhibition to catalytic domain dynamics
Relations
BioSample SAMN23796864
SRA SRX13355993

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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