Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Fetal_Liver_Gel_Velos

ABSTRACT: Fetal_Liver_Gel_Velos

REANALYSIS of: PXD000561

OTHER RELATED OMICS DATASETS IN: PXD000561MSV000079514E-PROT-1

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Liver

SUBMITTER: Pinto SM, Manda SS, Kim MS, Taylor K, Selvan LD, Balakrishnan L, Subbannayya T, Yan F, Prasad TS, Gowda H, Lee C, Hancock WS, Pandey A

PROVIDER: PAe004824 | PeptideAtlas | 2014-12-31

REPOSITORIES: PeptideAtlas

ACCESS DATA

Json Xml

Publications

Functional annotation of proteome encoded by human chromosome 22.

Pinto Sneha M SM Manda Srikanth S SS Kim Min-Sik MS Taylor KyOnese K Selvan Lakshmi Dhevi Nagarajha LD Balakrishnan Lavanya L Subbannayya Tejaswini T Yan Fangfei F Prasad T S Keshava TS Gowda Harsha H Lee Charles C Hancock William S WS Pandey Akhilesh A

Journal of proteome research 20140429 6

As part of the chromosome-centric human proteome project (C-HPP) initiative, we report our progress on the annotation of chromosome 22. Chromosome 22, spanning 51 million base pairs, was the first chromosome to be sequenced. Gene dosage alterations on this chromosome have been shown to be associated with a number of congenital anomalies. In addition, several rare but aggressive tumors have been associated with this chromosome. A number of important gene families including immunoglobulin lambda l ...[more]

PMID: 24669763

Similar Datasets

Silencing of TRIM28 in human iPSC

Project description:TRIM28, a multi-domain protein, is crucial in the development of mouse embryos and the maintenance of embryonic stem cells (ESC) self-renewal potential. As the epigenetic factor modulating the structure of chromatin, TRIM28 regulates the expression of numerous genes and is associated with progression and poor prognosis in many types of cancer. IPSC served as a model of the cells with stem cell-like phenotype, e.g., cancer stem cells. We evaluated the role of TRIM28 in pluripotency maintenance in iPSC by silencing endogenous TRIM28 expression with siRNA (iPSC-siTRIM28). IPSC treated with siRNA with no target sequence served as a control (siCTRL) of the experiment. Cells lacking TRIM28 lose the expression of pluripotency markers, as well as the ability to self-renew, and they start to differentiate. Pathway enrichment analysis using Gene Ontology datasets showed significant upregulation of pathways related to apoptosis, differentiation, cellular response to DNA damage stimulus and cell cycle regulation in iPSC-siTRIM28, relative to reference iPSC (iPSC-WT and iPSC-siCTRL).

2020-07-03 | GSE153726 | GEO

A primary Chlamydia trachomatis genital infection of Rhesus macaques identifies new immunodominant B-cell antigens

Project description:To identify immunodominant antigens that elicit a humoral immune response following a primary genital infection, rhesus monkeys were inoculated cervically with Chlamydia trachomatis serovar D. Serum samples were collected and probed with a protein microarray expressing 864/894 (96.4%) of the open reading frames of the C. trachomatis serovar D genome. The antibody response was analyzed in 72 serum samples from 12 inoculated monkeys. The following criteria were utilized to identify immunodominant antigens: proteins found to be recognized by at least 75% (9/12) of the infected monkeys with at least 15% elevations in normalized signal intensity from week 0 to week 8 post infection. All infected monkeys developed Chlamydia specific serum antibodies. Eight proteins satisfied the selection criteria for immunodominant antigens: CT242 (OmpH-like protein), CT541 (mip), CT681 (ompA), CT381 (artJ), CT443 (omcB), CT119 (incA), CT486 (fliY), and CT110 (groEL). Of these, three antigens, CT119, CT486 and CT381, were not previously identified as immunodominant antigens using non-human primate sera. In conclusion, these immunodominant antigens can now be tested for their ability to identify individuals with a primary C. trachomatis genital infection and to design a vaccine strategy to protect against a primary infection with this pathogen.

2020-05-27 | GSE151183 | GEO

Comprehensive Profiling of Rheumatoid Arthritis Antibody Repertoire

Project description:8 controls and 26 RA samples were profiled using NimbleTherapeutics high density peptide array. Array consists of >4.6M peptides, includes citrullination and homocitrullination against the entire human proteome represented as overlapping 16mer peptides.

2019-10-21 | GSE136052 | GEO

Multi Omics analysis of fibrotic kidneys in two mouse models (Unilateral ureter obstruction (UUO) model MS data set)

Project description:Kidney fibrosis represents an urgent unmet clinical need due to the lack of effective therapies and inadequate understanding of the molecular pathogenesis. We have generated a comprehensive and integrated multi-omics data set (proteomics, mRNA and small RNA transcriptomics) of fibrotic kidneys that is searchable through a user-friendly web application. Two commonly used mouse models were utilized: a reversible chemical-induced injury model (folic acid (FA) induced nephropathy) and an irreversible surgically-induced fibrosis model (unilateral ureteral obstruction (UUO)). mRNA and small RNA sequencing as well as 10-plex tandem mass tag (TMT) proteomics were performed with kidney samples from different time points over the course of fibrosis development. The bioinformatics workflow used to process, technically validate, and integrate the single data sets will be described. In summary, we present temporal and integrated multi-omics data from fibrotic mouse kidneys that are accessible through an interrogation tool to provide a searchable transcriptome and proteome for kidney fibrosis researchers.

2019-05-07 | GSE126182 | GEO

Multi Omics analysis of fibrotic kidneys in two mouse models (Folic acid (FA) model MS data set)

2019-05-07 | GSE126181 | GEO

Therapeutic antibodies to ganglioside GD2 evolved from highly selective germline antibodies

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-08-25 | GSE100438 | GEO

Therapeutic antibodies to ganglioside GD2 evolved from highly selective germline antibodies VI

Project description:Purpose: This study uses a high-throughput glycan microarray to evaluate the immunological evolution of antibodies to the glyco-antigen GD2. The goal is to determine germline and affinity mature antibody specificity and affinities/ Results: Affinity mature anti-GD2 antibodies 3F8 and ch14.18 had high affinity and were highly specific for the target GD2. Germline antibodies were also hihgly specific and had surprisingly high affinity. Conclusion: Antibodies to GD2 evolved from highly specific germlines. Highly specific germlines may be critical in evading autoimmunity issues.

2017-08-25 | GSE100309 | GEO

Antibody profile in patients with mild and severe leptospirosis

Project description:Leptospirosis is zoonotic disease of global importance, with over a million cases andnearly 60,000 deaths annually. Symptomatic disease presentation ranges from a mildfebrile disease with non-specific symptoms to severe forms, characterized by multi-organ failure, lung hemorrhage, and death. Factors governing severe outcomes remainunclear, but the host immune response likely plays an important role. In the presentstudy, we applied high throughput techniques to identify the antibody profiles ofpatients with severe and mild leptospirosis. We discovered a limited number ofimmunodominant antigens, specific to patients. Surprisingly, we found the antibodyrepertoire varies in patients with different clinical outcomes and hypothesized thatpatients with mild symptoms were protected from severe disease due to pre-existingantibodies, while the profile of patients with severe outcomes was representative of afirst exposure. These findings represent a substantial step forward in the knowledge ofthe humoral immune response to Leptospira infection, and we have identified newtargets for vaccine and diagnostic test development.

2016-09-10 | GSE86630 | GEO

A high throughput protein microarray approach to classify HIV monoclonal antibodies and variant antigens

Project description:In recent years, high throughput discovery of human recombinant monoclonal antibodies (mAbs) has been applied, to greatly advance our understanding of the specificity, and functional activity of antibodies, against HIV. Thousands of antibodies have been generated and screened in functional neutralization assays, and antibodies, associated with cross-strain neutralization and passive protection in primates, have been identified. To facilitate this type of discovery, a high throughput-screening tool is needed, to accurately classify mAbs, and their antigen targets. In this study, we analyzed and evaluated a prototype microarray chip, comprised of HIV-1 recombinant proteins gp140, gp120, gp41, and several membrane proximal external region peptides. The protein microarray analysis of 11 HIV-1 envelope-specific mAbs revealed diverse binding affinities and specificities across clades. Half maximal effective concentrations, generated by our chip analysis, correlated significantly (P<0.0001) with concentrations from ELISA binding measurements. Polyclonal immune responses in plasma samples, from HIV-1 infected subjects, exhibited different binding patterns and reactivity against printed proteins. Examining the totality of the specificity of the humoral response in this way reveals the exquisite diversity, and specificity of the humoral response to HIV.

2015-03-10 | GSE66659 | GEO

Genomic regions flanking E-box sites influence DNA binding specificity of bHLH transcription factors through DNA shape

Project description:This SuperSeries is composed of the SubSeries listed below.

2013-03-29 | GSE44604 | GEO