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RNA sequencing analysis for keratinocytes treated with U1 dsRNA and LL34 Alanine Scan Peptides

ABSTRACT: RNA sequencing analysis for keratinocytes treated with U1 dsRNA and LL34 Alanine Scan Peptides

PROVIDER: PRJNA705958 | ENA |

REPOSITORIES: ENA

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RNA sequencing analysis for keratinocytes treated with U1 dsRNA and LL34 Alanine Scan Peptides

Project description:Summary: We looked at the global changes in gene expression in keratinlcytes treated with selected LL34 Alanine mutants and U1 dsRNA. Methods: Normal human keratinocytes were treated with 2.5 ug/ml U1 dsRNA with or with out co-treatment with LL34 Parent Peptide/ LL34 I24A or LL34 L31A for 18 h. Conclusions: Global gene expression analysis showed pathways related to Type 1 interferon signaling and cytokines where mainly repressed in cells co-treated with either LL34 I24A/ LL34 L31A peptide and U1 dsRNA in comparision to cells co-treated with LL34-Parent peptide and U1 dsRNA.

2021-03-03 | GSE168050 | GEO

Alanine scan of 11 amino acid long novel linear epitope from C. jejuni cj0669 protein

Project description:A short sequence of 11 amino acids belonging to the cj0669 protein from Campylobacter jejuni NCTC 11168, which was previously identified as potentially immunogenic, was analyzed via alanine scanning to narrow down the significant amino acid residues within the sequence. Twelve peptides, one representing the original sequence and eleven peptides with each residue replaced by alanine in turn, were synthesized on microarrays by JPTs Pepstar Technology. For each microarray, nine replicates for each peptide were spotted. The microarray was separated into three incubation chambers by the ProPlate 3-well module (Grace Biolabs) to allow for incubation with different antibodies in parallel. For specific interactions, rabbit polyclonal IgG to C. jejuni was used, while unspecific binding to the epitope sequence was checked using rabbit polyclonal IgG to Salmonella enterica.

2013-04-06 | E-GEOD-45556 | biostudies-arrayexpress

Alanine scan of 11 amino acid long novel linear epitope from C.jejuni cj0669 protein [2]

Project description:A short sequence of 11 amino acids belonging to the cj0669 protein from Campylobacter jejuni NCTC 11168 which was previously identified as potentially immunogenig was analyzed via alanine scanning to narrow down the significant amino acid residues within the sequence. Twelve peptides, one representing the original sequence and eleven peptides with each residue replaced by alanine in turn, were synthesized on microarrays by JPTs Pepstar Technology. For each microarray, nine replicates for each peptide were spotted. The microarray was seperated into three incubation chambers by the ProPlate 3-well module (Grace Biolabs) to allow for incubation with different antibodies in parallel. For specific interaction rabbit polyclonal IgG to C.jejuni was used, while non-specific binding to the epitope sequence was checked using rabbit polyclonal IgG to H. pylori (Abcam ab20459).

2013-05-06 | E-GEOD-46651 | biostudies-arrayexpress

Alanine scan of potential linear epitopes of Klebsiella pneumoniae MGH 78578

Project description:Sequences of 11 amino acids belonging to the KPN_00363 protein and KPN_00459 protein from Klebsiella pneumoniae MGH 78578 which was previously identified as potentially immunogenic was analyzed via alanine scanning to narrow down the significant amino acid residues within the sequence.

2014-08-22 | GSE60588 | GEO

Alanine scan of 11 amino acid long novel linear epitope from C. jejuni cj0669 protein

2013-04-06 | GSE45556 | GEO

Alanine scan of 11 amino acid long novel linear epitope from C.jejuni cj0669 protein [2]

2013-05-06 | GSE46651 | GEO

Human dermal endothelial cells treated with sno U1 dsRNA and antimicrobial peptide LL-37

Project description:Next generation sequencing (RAN-seq) was used to study the global effects of co-treatment of endothelial cells with U1 and LL-37. This lead to identification of differentially regulated genes and enriched pathways

2019-04-02 | GSE129160 | GEO

Human dermal endothelial cells treated with sno U1 dsRNA and antimicrobial peptide LL-37

Project description:Human dermal endothelial cells treated with sno U1 dsRNA and antimicrobial peptide LL-37

| PRJNA530257 | ENA

Pro-inflammatory activity of SARS-CoV-2 viral peptide-dsRNA complex on human dermal microvascular endothelial cells (HDMVEC)

Project description:To investigate how SARS-CoV-2 viral peptides alter the immune sensing program in HDMVEC, we treated HDMVEC with SARS-CoV-2 viral peptide-dsRNA complex (xenoAMP(S)-dsRNA), Control(S)-dsRNA, dsRNA only or their associated controls. Control(S) was the homolog sequence of xenoAMP(S) from low pathogenic human coronavirus-OC43(HCoV-OC43). The gene expression profiles in the stimulated HDMVEC were analyzed with RNA sequencing.

2023-11-01 | GSE205487 | GEO

Platform comparison of U1 Adaptors - a new gene silencing technology vs. siRNA

Project description:The goal of the microarray experiment was to do a head-to-head comparison of the U1 Adaptor technology with siRNA in terms of specificity at the genome-wide level. U1 Adaptors represent a novel gene silencing method that employs a mechanism of action distinct from antisense and RNA interference (RNAi). The U1 Adaptor is a bifunctional oligonucleotide having a âTarget Domainâ that is complementary to a site in the target gene's terminal exon and a âU1 Domainâ that binds to the U1 small nuclear RNA (snRNA) component of the U1 small nuclear ribonucleoprotein (U1 snRNP) splicing factor. Tethering of U1 snRNP to the target pre-mRNA inhibits 3' end processing (i.e., polyA tail addition) leading to degradation of that RNA species within the nucleus thereby reducing mRNA levels. We demonstrate that U1 Adaptors can specifically inhibit both reporter and endogenous genes. Further, targeting the same gene either with multiple U1 Adaptors or with U1 Adaptors and small interfering RNAs (siRNAs), strongly enhances gene silencing, the latter as predicted from their distinct mechanisms of action. Such combinatorial targeting requires lower amounts of oligonucleotides to achieve potent silencing. Experiment Overall Design: For each sample total RNA was prepared from 3 independent transfections and then were pooled and analyzed by QPCR and also by microarray.

2009-02-21 | E-GEOD-14434 | biostudies-arrayexpress

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