Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Generation of highly diverse peptide library by linear-double-stranded DNA based AND gate genetic circuit in mammalian cells

ABSTRACT: Generation of highly diverse peptide library by linear-double-stranded DNA based AND gate genetic circuit in mammalian cells

PROVIDER: PRJEB33584 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Construction of Nanobody Library in Mammalian Cells by Linear-double-stranded DNA Based AND Gate Genetic Circuit

Project description:Nanobody is one special type of single-domain antibody fragment with multiple advantages over traditional antibody. Our previous work established linear-double-stranded DNA (ldsDNA, or PCR amplicon) as novel biological parts for building AND gate genetic circuits in mammalian cells. During this AND-gate circuit formation process, the co-transfected up- and down-stream ldsDNAs could be linked together to form intact gene expression cassette. Here, we employed this ldsDNA-based AND-gate (LBAG) strategy to construct nanobody library in mammalian cells. The sequence complexity of complementary determining regions (CDRs) was introduced into ldsDNA by PCR amplification. After being co-transfected into mammalian cells, the up- and down- stream ldsDNAs undergo AND gate linkage and form full nanobody coding regions, containing CDR1-3. High throughput sequencing identified 22,173 unique oligonucleotide sequences in total generated by this strategy. Thus, we developed a novel method to construct nanobody library, which is a start point for building high content nanobody library in mammalian cells.

2021-07-24 | GSE155159 | GEO

Generation of highly diverse peptide library by linear-double-stranded DNA based AND gate genetic circuit in mammalian cells

Project description:Display technologies, e.g., phage, ribosome, mRNA, bacterial, and yeast-display, combine high content peptide libraries with appropriate screening strategies to identify functional peptide sequences. Construction of large peptide library and display-screen system in intact mammalian cells will facilitate the development of peptide therapeutics targeting transmembrane proteins. Our previous work established linear-double-stranded DNAs (ldsDNAs) as innovative biological parts to implement AND gate genetic circuits in mammalian cell line. In the current study, we employ ldsDNA with terminal NNK degenerate codons as AND gate input to build highly diverse peptide library in mammalian cells. Only PCR reaction and cell transfection experiments are needed to construct the library. High-throughput sequencing (HTS) results reveal that our new strategy could generate peptide library with both amino acid sequence and peptide length diversities. Our work establishes ldsDNA as biological parts for building highly diverse peptide library in mammalian cells, which shows great application potential in developing therapeutic peptides targeting transmembrane proteins.

2020-07-19 | GSE134671 | GEO

Generation of highly diverse peptide library by linear-double-stranded DNA based AND gate genetic circuit in mammalian cells

Project description:Generation of highly diverse peptide library by linear-double-stranded DNA based AND gate genetic circuit in mammalian cells

| PRJNA556026 | ENA

Construction of Nanobody Library in Mammalian Cells by Linear-double-stranded DNA Based AND Gate Genetic Circuit

Project description:Construction of Nanobody Library in Mammalian Cells by Linear-double-stranded DNA Based AND Gate Genetic Circuit

| PRJNA648873 | ENA

Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage

Project description:When performing a computation, genetic circuits change states through a symphony of genetic parts that turn regulator expression on and off. Debugging is frustrated by an inability to measure part function and identify the origins of failures. Here, we take “snapshots” of a large genetic circuit in different states. RNA-seq is used to visualize circuit function as a changing pattern of RNA polymerase (RNAP) flux along the DNA. Together with ribosome profiling, all 54 genetic parts are parameterized. The circuit behaves as designed; however, it is riddled with errors, including cryptic sense/antisense promoters and translation, attenuation, incorrect start codons and a failed gate. While serendipitously not impacting function, they reduce prediction accuracy and could lead to failures when used in other designs. Finally, the cellular power (RNAPs and ribosomes) required to maintain a circuit state is calculated. This work demonstrates the use of a small number of measurements to fully parameterize a regulatory circuit and quantify its impact on host.

2020-06-18 | GSE152664 | GEO

Devil's Gate

Project description:Sequence data from Neolithic (7,700BP) hunter-gatherer samples from Devil's Gate, East Asia.

| PRJEB14810 | ENA

caArray_laird-00051: TCGA Analysis of DNA Methylation for GBM Using Illumina Golden Gate BeadArray platform

Project description:TCGA Analysis of DNA Methylation for GBM Using Illumina Golden Gate BeadArray platform

2015-11-21 | GSE75244 | GEO

caArray_laird-00098: TCGA Analysis of DNA Methylation for GBM Using Illumina Golden Gate BeadArray platform (IlluminaDNAMethylation_OMA003_CPI)

Project description:TCGA Analysis of DNA Methylation for GBM Using Illumina Golden Gate BeadArray platform

2015-11-21 | GSE75254 | GEO

Effect of Oral Administration of Methylene Blue MMX Tablets on Double Stranded DNA

Project description:Single Centre, open label assignment phase II clinical study. To evaluate the effect of oral 200mg Methylene Blue tablets (administered 8x25mg) prior to endoscopy on double stranded DNA breaks in colonic biopsy samples assessed by histone gamma H2AX analysis, compared to control biopsies.

| 2178654 | ecrin-mdr-crc

TEBP-1 and TEBP-2 are double-stranded telomere binders required for fertility

Project description:Telomeres are the ends of linear chromosomes and consist of repetitive double- and single-stranded DNA sequences. Telomeres are bound by dedicated protein complexes, such as shelterin in mammals. In the nematode Caenorhabditis elegans, a comprehensive understanding of the proteins interacting with the telomere sequence is lacking. Here, we harnessed a quantitative proteomics approach to screen for proteins binding to C. elegans telomeres, and identified TEBP-1 and TEBP-2, two paralogs that associate to telomeres in vitro and in vivo. TEBP-1 and TEBP-2 form a telomeric complex with the known single-stranded telomere-binding proteins POT-1, POT-2, and MRT-1. tebp-1 and tebp-2 mutants display strikingly distinct phenotypes: tebp-1 mutants have longer telomeres than wild-type animals, while tebp 2 mutants display shorter telomeres and a mortal germline, a phenotype characterized by transgenerational germline deterioration. Notably, tebp 1;tebp-2 double mutant animals are synthetic sterile, with germlines showing signs of severe mitotic and meiotic arrest. These results define the first telomere-binding complex of C. elegans, including TEBP-1 and TEBP-2, two double-stranded telomere binders required for fertility.

2021-03-09 | PXD019241 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data