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Sample GSM7806611

Query DataSets for GSM7806611

Status

Public on Sep 28, 2023

Title

PSD95-PDZ3_bPCA_output_bio_rep_2

Sample type

SRA

Source name

BY4741

Organism

Saccharomyces cerevisiae

Characteristics

strain: BY4741
protein domains: PSD95-PDZ
assays: binding PCA
subtype: DNA amplicon

Growth protocol

For each of the two protein domains (GRB2-SH3 and PSD95-PDZ) and the pooled libraru (7-doms) for both the aPCA and bPCA assays (abundancePCA and bindingPCA), each of the growth competitions was performed right after yeast transformation. After the first cycle of post-transformation plasmid selection, a second plasmid selection cycle (input) was performed by inoculating SC -URA/ADE at a starting OD600nm = 0.1 with the saturated culture. Cells were grown for 4 generations at 30ºC under constant agitation at 200 rpm. This allowed the pool of mutants to be amplified and enter the exponential growth phase. The competition cycle (output) was then started by inoculating cells from the input cycle into the competition media (SC -URA/ADE + 200 ug/mL Methotrexate) so that the starting OD600nm was 0.05. For that, the adequate volume of cells were collected, centrifuged at 3,000 rpm for 5 minutes and resuspended in the pre-warmed output media. Meanwhile, each input replicate culture was splitted in two and harvested by centrifugation for 5 min at 5,000g at 4ºC. Yeast cells were washed with water, pelleted and stored at -20ºC for later DNA extraction. After ~5 generations of competition cycle, each output replicate culture was splitted into two and harvested by centrifugation for 5 min at 5,000g at 4ºC, washed twice with water and pelleted to be stored at -20ºC

Extracted molecule

genomic DNA

Extraction protocol

Cell pellets (one for each experiment input/output replicate) were re-suspended in 1 mL of DNA extraction buffer (2% Triton-X, 1% SDS, 100mM NaCl, 10mM Tris-HCl pH8, 1mM EDTA pH8), frozen by dry ice-ethanol bath and incubated at 62ºC water bath twice. Subsequently, 1 mL of Phenol/Chloro/Isoamyl 25:24:1 (equilibrated in 10mM Tris-HCl, 1mM EDTA, pH8) was added, together with 1 g of acid-washed glass beads (Sigma Aldrich) and the samples were vortexed for 10 minutes. Samples were centrifuged at RT for 30 minutes at 4,000 rpm and the aqueous phase was transferred into new tubes. The same step was repeated twice. 0.1 mL of NaOAc 3M and 2.2 mL of pre-chilled absolute ethanol were added to the aqueous phase. The samples were gently mixed and incubated at -20ºC for 30 minutes. After that, they were centrifuged for 30 min at full speed at 4ºC to precipitate the DNA. The ethanol was removed and the DNA pellet was allowed to dry overnight at RT. DNA pellets were resuspended in 0.6 mL TE 1X and treated with 5 uL of RNaseA (10mg/mL, Thermo Scientific) for 30 minutes at 37ºC. To desalt and concentrate the DNA solutions, QIAEX II Gel Extraction Kit was used (30 μL of QIAEX II beads). The samples were washed twice with PE buffer and eluted twice by 125 μL of 10 mM Tris-HCI buffer, pH 8.5 and then combined two elution. Finally, plasmid concentrations in the total DNA extract (that also contained yeast genomic DNA) were quantified by qPCR using the primer pair oGJJ152-oGJJ153, that binds to the ori region of the plasmids.
We performed 2 consecutive PCR reactions for each sample. The first PCR (PCR1) is used to amplify the amplicons for sequencing, to add a part of the illumina sequencing adaptors to the amplicon and to increase nucleotide complexity for the sequencing reaction by introducing frame-shift bases between the adapters and the sequencing region of interest. The second PCR (PCR2) is used to add the remainder of the illumina adaptor and to add demulitplexing indexes. All samples, except the GRB2-SH3 bPCA, were dual-indexed using differing barcode indexes both for the forward (5’ P5 Illumina adapter) and reverse oligos (3’ P7 Illumina adapter). The GRB2-SH3 bPCA library was single-indexed using a constant forward oligo (3’ P7 Illumina adapter) and alternating reverse oligos (3’ P7 Illumina adapter). The amplicon library pools were run on a 2% agarose gel and were purified using QIAEX II Gel Extraction Kit (QIAGEN) and using 30uL of QIAEX II beads for each sample. The purified amplicons were subjected to Illumina 150bp paired-end NextSeq sequencing at the CRG Genomics Core Facility.

Library strategy

OTHER

Library source

genomic

Library selection

other

Instrument model

NextSeq 2000

Description

scaled_variants_bPCA.xls

Data processing

DiMSum (Demultiplex with Cutadapt)
DiMSum (QC raw reads with FastQC)
DiMSum (Trim reads with Cutadapt)
DiMSum (Process and analyse variants with DiMSum)
Supplementary files format and content: Tabular format; contains the Dimsum fitness estimations and their corresponding errors
Library strategy: DNA-seq

Submission date

Sep 26, 2023

Last update date

Sep 28, 2023

Contact name

Magdalena Topolska

Organization name

Centre for Genomic Regulation

Department

Systems and Synthetic Biology

Lab

Ben Lehner