Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Stapled phage-displayed peptide library selections of D-MDM2 and D-CHIP

PROVIDER: PRJNA997450 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR25388900.fastq.gz	Fastqsanger.gz
	SRR25388901.fastq.gz	Fastqsanger.gz
	SRR25388902.fastq.gz	Fastqsanger.gz
	SRR25388903.fastq.gz	Fastqsanger.gz
	SRR25388904.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 14

Similar Datasets

Effect of the Foxp3 inhibitory peptide P60 on gene array expression of Karpas cell line

Project description:By using a phage displayed peptide library we identified peptide P60 as able to bind Foxp3 and inhibit Treg activity. To gain insight into the effect of P60 in Foxp3+ve cells we used Karpas 299 human cell line derived from a human lymphoma with a regulatory T cell profile. Microarray analysis of Karpas cell line incubated with or without P60 peptide was carried out using the Affymetrix human U133 Plus 2.0 array.

2024-01-21 | GSE165260 | GEO

Project description:Synthetic library construct of a peptide-HLA library displayed in yeast, selected by TCR

| PRJNA438012 | ENA

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

Peptide gene sequences of substrate phage for different proteases

Project description:We present a method that employs two genetically encoded substrate phage display libraries coupled with next generation sequencing (SPD-NGS) that allows up to 10,000-fold deeper sequence coverage of the typical 6 to 8 residue protease cleavage sites compared to state-of-the-art synthetic peptide libraries or proteomics. We applied SPD-NGS to two classes of proteases, the intracellular caspases 2, 3, 6, 7 and 8, and the ectodomains of the membrane sheddases, ADAMs 10 and 17. The first library (Lib 10AA) was used to determine substrate cleavage motifs. Lib 10AA contains a highly diverse randomized 10-mer substrate peptide sequences (10^9 unique members) that was displayed mono-valently on filamentous phage and bound to magnetic beads via an N-terminal biotin. The protease was allowed to cleave the SPD beads, and the released phage subjected to up to three total rounds of positive selection followed by next generation sequencing (NGS). This allowed us to identify from 10^4 to 10^5 unique cleavage sites over a broad dynamic range of NGS counts (ranging from 3-5000), and produced consensus and optimal cleavage motifs based positional sequencing scoring matrices and state-of the-art machine learning algorithm that closely matched synthetic peptide data. A second SPD-NGS library (Lib hP) was constructed that allowed us to identify candidate human proteome sequences. Lib hP displayed virtually the entire human proteome tiled in contiguous 49AA sequences with 25AA overlaps (nearly 1 million members). After three rounds of positive selection we identified up to 10^4 natural linear cut sites depending on the protease and captured most of the examples previously identified by proteomics (ranging from 30 to 1000) and predicted 10 to 100-fold more.

2020-07-23 | GSE154923 | GEO

Effect of LPS, sHVF18 and the combination therof on gene expression in murine lungs

Project description:Excessive Toll-like receptor (TLR) and NF-kB activation during infection causes the overactivation of inflammatory pathways seen in sepsis. Thrombin-derived C-terminal peptides (TCPs) target both bacteria and the resulting TLR-mediated inflammatory response during infection. The present study describes the design and development of a novel multifunctional stapled peptide mimicking the actions of such immunomodulatory TCPs, providing a new drug class based on nature’s own anti-infective strategies. Using a combination of structure-based design, nuclear magnetic resonance spectroscopy (NMR), biophysics, mass spectrometry, microbiology, cellular, and in vivo studies, we describe the development of a structurally locked active stapled form of the endogenous peptide HVFRLKKWIQKVIDQFGE, denoted sHVF18. The stapled peptide shows a higher affinity to CD14 than the linear peptide, retains a partly helical and stabilized structure, and is protease resistant. In vivo, it shows efficacy in experimental models of endotoxin shock in mice and pigs and increases survival in mouse models of polymicrobial sepsis.

2024-01-01 | GSE217695 | GEO

DNA sequencing for multiple rounds of the pMHC-yeast display selection for TCR6, TCR7 and FluTCR [other]

Project description:A peptide library was displayed on Db MHC class I allele expressed on yeast. TCRs of interest were used to select and enrich for cognate peptide-MHC.

2020-01-01 | GSE133363 | GEO

DNA sequencing for multiple rounds of the pMHC-yeast display selection for 2W, Yae and Fat TCR

Project description:A peptide library was displayed on Ab MHC class II allele expressed on yeast. TCRs of interest were used to select and enrich for cognate peptide-MHC.

2020-06-15 | GSE151070 | GEO

Project description:Synthetic library construct of a peptide-HLA-A*01 library displayed in yeast, selected by A3a TCR

| PRJNA664818 | ENA

NGS of phage antibody outputs from whole-cell panning

Project description:We present a target-unbiased approach for antibody discovery that relies on generating mAbs against native target cell surfaces via phage display. This method combines a previously reported method for improved whole-cell phage display selections with next-generation sequencing analysis to efficiently identify mAbs with the desired target cell reactivity. This approach enabled the identification of three multiple myeloma cell surface antigens, and cognate monoclonal antibody probes.

2023-01-18 | GSE222897 | GEO

Project description:Biopanning of phage-displayed peptides

| PRJNA884199 | ENA