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Sample GSM5646616 Query DataSets for GSM5646616
Status Public on Oct 31, 2023
Title SC_high
Sample type SRA
 
Source name Synthetic construct
Organism Saccharomyces cerevisiae
Characteristics strain: S288C
genotype: wild type
plasmid type: reporter gene with synthetic NCS
expression level: high
Extracted molecule other
Extraction protocol After FACS-sorting and overnight regrowth in the same media used for growth, sorted fractions were miniprepped. PCR was used to verify that at least 10 plasmids were extracted per sorted cell; minipreps were PCR-amplified, further amplified with the addition of bin-specific barcodes, pooled, and amplified briefly again.
For each sample, >50ng purified PCR fragment was used for library preparation. These PCR products were treated with End Prep Enzyme Mix for end repairing, 5’ Phosphorylation and dAtailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Adaptor-ligated DNA was then performed using DNA Clean Beads. A second PCR reaction was carried out with P5 and P7 primers carrying sequences which can anneal with flowcell to perform bridge PCR and index allowing for multiplexing. The final library product for sequencing were then purified by beads and was qualified.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Cutadapt is applied to find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
PANDASEQ is used to assemble paired-end Illumina reads into sequences, trying to correct for errors and uncalled bases.
Genome_build: NCBI number: AF330636.1
Supplementary_files_format_and_content: csv files include filtered sequences
 
Submission date Oct 22, 2021
Last update date Oct 31, 2023
Contact name Yanfeng Liu
E-mail(s) yanfengliu@jiangnan.edu.cn
Phone 86-510-85197117
Organization name Jiangnan University
Street address No.1800, Lihu Avenue
City Wuxi
State/province Jiangsu
ZIP/Postal code 214122
Country China
 
Platform ID GPL27812
Series (1)
GSE186378 Model-driven design of synthetic N-terminal coding sequences for fine-tuning gene expression in yeast and bacteria
Relations
BioSample SAMN22504096
SRA SRX12734808

Supplementary file Size Download File type/resource
GSM5646616_filtered_SC_High.csv.gz 25.0 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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