Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26135800.fastq.gz | Fastqsanger.gz | |||
| SRR26135801.fastq.gz | Fastqsanger.gz | |||
| SRR26135802.fastq.gz | Fastqsanger.gz | |||
| SRR26135803.fastq.gz | Fastqsanger.gz | |||
| SRR26135804.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:phage ORF screen
| PRJEB58053 | ENA
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:Single cell multi-omic readouts of both the cellular transcriptome and proteome have significantly enhanced our ability to comprehensively characterize cellular states. Most approaches in this area rely on oligonucleotide barcode-conjugated antibodies that target cell surface epitopes of interest, enabling their concomitant detection with the transcriptome. However, a similar high-throughput measurement of other cellular modalities such as the epigenome in concert with protein levels have not been described. Moreover, detection of epitopes is limited to antigens for which a specific antibody is available. Here, we introduce PHAGE-ATAC, an approach that enables the scalable and simultaneous detection of protein levels and chromatin accessibility data in single cells using the assay of transposase-accessible chromatin with sequencing (ATAC-seq). Quantitative detection of proteins by PHAGE-ATAC is accomplished through the use of engineerable nanobody-displaying phages that are genetically barcoded within the nanobody-encoding phagemids. We demonstrate the utility of PHAGE-ATAC for multimodal single cell genomic analysis in both cell lines and primary human cells. Analogous to phage display approaches, we further establish a synthetic high-complexity library of nanobody-displaying phages and demonstrate its utility to select novel antigen-specific nanobodies for PHAGE-ATAC.
2021-10-21 | GSE157485 | GEO
Project description:Single cell multi-omic readouts of both the cellular transcriptome and proteome have significantly enhanced our ability to comprehensively characterize cellular states. Most approaches in this area rely on oligonucleotide barcode-conjugated antibodies that target cell surface epitopes of interest, enabling their concomitant detection with the transcriptome. However, a similar high-throughput measurement of other cellular modalities such as the epigenome in concert with protein levels have not been described. Moreover, detection of epitopes is limited to antigens for which a specific antibody is available. Here, we introduce PHAGE-ATAC, an approach that enables the scalable and simultaneous detection of protein levels and chromatin accessibility data in single cells using the assay of transposase-accessible chromatin with sequencing (ATAC-seq). Quantitative detection of proteins by PHAGE-ATAC is accomplished through the use of engineerable nanobody-displaying phages that are genetically barcoded within the nanobody-encoding phagemids. We demonstrate the utility of PHAGE-ATAC for multimodal single cell genomic analysis in both cell lines and primary human cells. Analogous to phage display approaches, we further establish a synthetic high-complexity library of nanobody-displaying phages and demonstrate its utility to select novel antigen-specific nanobodies for PHAGE-ATAC.
2021-10-21 | GSE157483 | GEO
Project description:Single cell multi-omic readouts of both the cellular transcriptome and proteome have significantly enhanced our ability to comprehensively characterize cellular states. Most approaches in this area rely on oligonucleotide barcode-conjugated antibodies that target cell surface epitopes of interest, enabling their concomitant detection with the transcriptome. However, a similar high-throughput measurement of other cellular modalities such as the epigenome in concert with protein levels have not been described. Moreover, detection of epitopes is limited to antigens for which a specific antibody is available. Here, we introduce PHAGE-ATAC, an approach that enables the scalable and simultaneous detection of protein levels and chromatin accessibility data in single cells using the assay of transposase-accessible chromatin with sequencing (ATAC-seq). Quantitative detection of proteins by PHAGE-ATAC is accomplished through the use of engineerable nanobody-displaying phages that are genetically barcoded within the nanobody-encoding phagemids. We demonstrate the utility of PHAGE-ATAC for multimodal single cell genomic analysis in both cell lines and primary human cells. Analogous to phage display approaches, we further establish a synthetic high-complexity library of nanobody-displaying phages and demonstrate its utility to select novel antigen-specific nanobodies for PHAGE-ATAC.
2021-10-21 | GSE157478 | GEO
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
Project description:IgNAR exhibits significant promise in the fields of cancer and anti-virus biotherapies. Notably, the variable regions of IgNAR (VNAR) possess comparable antigen binding affinity with much smaller molecular weight (~12 kDa) compared to IgNAR. Antigen specific VNAR screening is a changeling work, which limits its application in medicine and therapy fields. Though phage display is a powerful tool for VNAR screening, it has a lot of drawbacks, such as small library coverage, low expression levels, unstable target protein, complicating and time-consuming procedures. Here we report VNAR screening with next generation sequencing (NGS) could effectively overcome the limitations of phage display, and we successfully identified approximately 3000 BAFF-specific VNARs in Chiloscyllium plagiosum vaccinated with the BAFF antigen. The results of modelling and molecular dynamics simulation and ELISA assay demonstrated that one out of the top five abundant specific VNARs exhibited higher binding affinity to the BAFF antigen than those obtained through phage display screening. Our data indicates NGS would be an alternative way for VNAR screening with plenty of advantages.
2024-01-01 | GSE249557 | GEO
Project description:Interventions: Gold Standard:Body temperature monitoring.;Index test:a double-needle temperature probe (BeneView T8, Mindray Display Screen, Shenzhen, China) placed in the nasopharynx.
Primary outcome(s): hypothermia
Study Design: Sequential
| 2760520 | ecrin-mdr-crc
Project description:High-density phage epitope microarray from 31 samples were used for unsupervised analysis (GSM36153...GSM36183). 129 samples from prostate cancer patients and controls were screened on small focused epitope chips, which contained 180 phage elements. These data were used to train GA/KNN program (GSM36184...GSM36312). 128 samples from localized prostate cancer patients and controls were screened on small focused epitope chips. These independent data were used to validate the epitomic profile (GSM36313...GSM36375, GSM40203...GSM40213, GSM40216, GSM40218, GSM40219, GSM40222, GSM40225, GSM40227, GSM40229, GSM40233, GSM40237, GSM40246...GSM40294). Three subgroups of samples were used as test sets to validate the specificity of epitomic profile (GSM36376...GSM36410, GSM40214, GSM40215, GSM40217, GSM40220, GSM40221, GSM40224, GSM40226, GSM40228, GSM40231, GSM40234...GSM40236, GSM40238...GSM40244). Project----Identification of humoral signature for prostate cancer diagnosis We constructed a prostate cancer cDNA phage display library. cDNAs were reverse-synthesized from mDNA pool isolated from prostate cancer tissues. Enzyme-digested cDNA fragments were then inserted into phage vector to make a whole prostate cancer phage expressed cDNA library. In order to select cancer specific phage epitope from this library, we performed several cycles of affinity enrichment. We used the bounded IgG pool isolated from prostate cancer patient sera to select the tumor specific phage epitope clones. Once we had the enriched phage epitope library, we cultured the phage library on LB-agar dish for individual phage colonies. About 2300 phage colonies from agar dish were picked up using toothstick and cultured in 96-well microtiter plates. Each clone was labeled as microtiter plate #, column #, row#, i.e. clone ID. These 2300 clones were then spotted on slides in single spot (no any duplicate), i.e. each spot (labeled by clone ID) represents a single phage clone. The phage epitope microarrays were then screened using cancer or control sera. We employed two color system. Cy5-anti human IgG was to detect human IgG. For green color, we used Cy3-labeled anti-phage capsid protein as internal reference to normalize the ammount difference of phage particles spotted on each spot. Thus the ratio of Cy5/Cy3 would count for the immune response in cancer or control sera. Once we identified humoral signature in prostate cancer patients, we could sequence the phage clone to characterize the nature of the genes or proteins.
2005-10-04 | E-GEOD-2010 | biostudies-arrayexpress