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GEO help: Mouse over screen elements for information. |
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Status |
Public on Oct 31, 2023 |
Title |
SC_high |
Sample type |
SRA |
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Source name |
Synthetic construct
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Organism |
Saccharomyces cerevisiae |
Characteristics |
strain: S288C genotype: wild type plasmid type: reporter gene with synthetic NCS expression level: high
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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.
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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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
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Submission date |
Oct 22, 2021 |
Last update date |
Oct 31, 2023 |
Contact name |
Yanfeng Liu |
E-mail(s) |
yanfengliu@jiangnan.edu.cn
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Phone |
86-510-85197117
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Organization name |
Jiangnan University
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Street address |
No.1800, Lihu Avenue
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City |
Wuxi |
State/province |
Jiangsu |
ZIP/Postal code |
214122 |
Country |
China |
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Platform ID |
GPL27812 |
Series (1) |
GSE186378 |
Model-driven design of synthetic N-terminal coding sequences for fine-tuning gene expression in yeast and bacteria |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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