Project description:Purpose:The aim of this study is to evaluate the characteristics of hnRNP U binding site. Methods: The chromatin of BNL CL.2 cells was immunoprecipitated with anti-hnRNP U(Abcam) and normal rabbit immunoglobulin G (IgG). The immunoprecipitated DNA was then subjected to various previously constructed sequencing libraries. The libraries were sequenced using the Illumina Hiseq2500. All reads were aligned to the mm9 genome browser using the bowtie with default parameters. Results: A total number of 12249 peaks that specifically binded by hnRNP U was obtained. Conclusions: Our study represents the first detailed analysis of genome-wide binding sites of hnRNP U generated by ChIP-seq technology. hnRNP U binding profiling in Mus musculus fetal liver cell line BNL CL.2 cells, and the IgG antibody was used as a negative control

2015-11-25 | E-GEOD-75335 | biostudies-arrayexpress

An interspecies analysis reveals sequence determinants of the bivalent chromatin state

Project description:The sequence determinants of chromatin bivalency remain unclear. We analysed sequence determinants of chromatin bivalency genome-wide in several mammalian species and performed a series of transgenic experiments in mouse ES cells. Genome-wide mapping of H3K27me3 in rat ES cells and ChIP-seq with anti-Ezh2 antibody in transgenic mouse ES cells

2011-11-16 | E-GEOD-27580 | biostudies-arrayexpress

Global Analyses of Human Immune Variation Reveal Baseline Predictors of Postvaccination Responses

Project description:A major goal of systems biology is the development of models that accurately predict responses to perturbation. Constructing such models requires the collection of dense measurements of system states, yet transformation of data into predictive constructs remains a challenge. To begin to model human immunity, we analyzed immune parameters in depth both at baseline and in response to influenza vaccination. Peripheral blood mononuclear cell transcriptomes, serum titers, cell subpopulation frequencies, and B cell responses were assessed in 63 individuals before and after vaccination and were used to develop a systematic framework to dissect inter- and intra-individual variation and build predictive models of postvaccination antibody responses. Strikingly, independent of age and pre-existing antibody titers, accurate models could be constructed using pre-perturbation cell populations alone, which were validated using independent baseline time points. Most of the parameters contributing to prediction delineated temporally stable baseline differences across individuals, raising the prospect of immune monitoring before intervention.

2014-04-10 | GSE47353 | GEO

Antibody Dependent Cell-Mediated Cytotoxicity Selection Pressure Induces Diverse Mechanisms of Resistance (scATAC-Seq)

Project description:Targeted monoclonal antibody therapy has emerged as a powerful therapeutic strategy for cancer. Unfortunately, only a minority of patients haves durable responses and the development of resistance remains a major clinical obstacle. Antibody-dependent cell-mediated cytotoxicity (ADCC) represents a crucial therapeutic mechanism of action; however few studies have explored ADCC resistance. Using multiple in vitro models of ADCC selection pressure, we have uncovered both shared and distinct resistance mechanisms. We employed CITE sequencing and single-cell ATAC-seqeuncing to interrogate molecular mechanisms of resistance.

2023-11-13 | GSE206954 | GEO

Global analyses of human immune variation reveal baseline predictors of the post-vaccination response.

Project description:A major goal of systems biology is the development of models that accurately predict responses of a cell or organism to perturbation. Constructing such models requires collection of dense measurements of system states, yet transformation of the data into predictive constructs remains a challenge. As a first step towards modeling human immunity, we have analyzed immune parameters in depth both at baseline and in response to perturbation with influenza vaccination. Peripheral blood cell transcriptomes, serum titers, frequencies of 126 cell subpopulations, and B cell responses were assessed before and after vaccination in 63 individuals and used to develop a systematic, computational framework to dissect inter- and intra-individual variation and build predictive models of post-vaccination antibody responses. Strikingly, independent of age and pre-existing antibody titers, accurate models could be constructed using pre-perturbation parameters alone, which were validated using data from independent baseline time-points. Most of the parameters contributing to prediction delineated temporally-stable baseline differences across individuals, raising the prospect of immune responsiveness prediction before intervention. According to CHI protocol 09-H1-0239, PBMC samples from 63 healthy voluntiers were collected 7 days prior to vaccination, immediately before vaccination (day0), and at 3 time points (day1, day7 and day70) post vaccination. The CHI Consortium

2014-04-10 | E-GEOD-47353 | biostudies-arrayexpress

Deciphering and predicting CD4+ T cell immunodominance of Influenza virus hemagglutinin

Project description:The importance of CD4+ T helper (Th) cells is well appreciated in view of their essential role in the elicitation of antibody and cytotoxic T cell responses. However, the mechanisms that determine the selection of immunodominant epitopes within complex protein antigens remain elusive. Here, we used ex vivo stimulation of memory T cells and screening of naïve and memory T cell libraries, combined with T cell cloning and TCR sequencing, to dissect the human naïve and memory CD4+ T cell repertoire against the influenza pandemic H1 hemagglutinin (H1-HA). We found that naïve CD4+ T cells have a broad repertoire, being able to recognize naturally processed as well as cryptic peptides spanning the whole H1-HA sequence. In contrast, memory Th cells were primarily directed against just a few immunodominant peptides that were readily detected by mass spectrometry-based MHC-II peptidomics and predicted by structural accessibility analysis. Collectively, these findings reveal the presence of a broad repertoire of naïve T cells specific for cryptic H1-HA peptides, and demonstrate that antigen processing represents a major constraint determining immunodominance.

2020-06-29 | PXD018151 | Pride

A Unifying Model for Molecular Determinants of the Pre-selection Vβ Repertoire [ChIP-chip]

Project description:Chip-chip from pro-T(DN) cells from Rag1KO mice for H3K27ac, P300 and FAIRE The primary antigen receptor repertoire is sculpted by the process of V(D)J recombination, which must strike a balance between diversification and favoring gene segments with specialized functions. The precise determinants of how often gene segments are chosen to complete variable region coding exons remain elusive. We have quantified Vβ usage in the pre-selection Tcrb repertoire and report relative contributions of 14 distinct features in shaping their recombination efficiencies, including transcription, chromatin environment, spatial proximity to their DβJβ targets, and quality of recombinase recognition elements. Computational analyses provide a unifying model, revealing a minimal set of eight parameters that are predictive of Vβusage, dominated by chromatin modifications associated with transcription, but largely independent of the precise spatial proximity to DβJβclusters.

2013-08-14 | GSE42851 | GEO

Escherichia phage T7

Project description:Deep sequencing of antibody enrichment with Phage-DMS libraries

| PRJNA630833 | ENA