Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Reanalysis of NOD mouse insulin granule and secreted peptidome data

ABSTRACT: Data from a previous publication from our lab (Nature 2018 Aug; 560 (7716): 107-111) were reanalyzed by performing a multiround search against a Uniprot-Mouse database followed by an in silico database of hybrid insulin peptides.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Cell Culture, Secretory Granule, Pancreatic Islet Beta Cell

DISEASE(S): Type 1 Diabetes Mellitus

SUBMITTER: Cheryl Lichti

LAB HEAD: Cheryl Lichti

PROVIDER: PXD015726 | Pride | 2020-03-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Delong_HIP_Human.fasta	Fasta
	MouseProteome-OnePerGene_022519.fasta	Fasta
	Unanue_170807_06.mgf	Mgf
	Unanue_170807_06.pride.mgf.gz	Mgf
	Unanue_170807_06.raw	Raw

Items per page:

1 - 5 of 44

Publications

The MHC-II peptidome of pancreatic islets identifies key features of autoimmune peptides.

Wan Xiaoxiao X Vomund Anthony N AN Peterson Orion J OJ Chervonsky Alexander V AV Lichti Cheryl F CF Unanue Emil R ER

Nature immunology 20200309 4

The nature of autoantigens that trigger autoimmune diseases has been much discussed, but direct biochemical identification is lacking for most. Addressing this question demands unbiased examination of the self-peptides displayed by a defined autoimmune major histocompatibility complex class II (MHC-II) molecule. Here, we examined the immunopeptidome of the pancreatic islets in non-obese diabetic mice, which spontaneously develop autoimmune diabetes based on the I-A<sup>g7</sup> variant of MHC-II ...[more]

PMID: 32152506

Similar Datasets

Reanalysis of ChIP-Seq of GSE117155.

Project description:In this reanalysis, 20 GSM series were reanalyzed for ChIp-Seq data.

2023-12-01 | GSE248645 | GEO

Reanalysis of TSA-Seq mapping to determine genomic coordinates for speckles-associated domains.

Project description:In this reanalysis, 9 GSM series were reanalyzed to obtain the genomic coordinates of speckles-associated domains.

2023-12-01 | GSE248644 | GEO

Variation and genetic control of chromatin architecture in humans (RNAseq)

Project description:This data set comprises population (46 samples) measurements of RNA expression levels for a subset of the 1000 Genomes Project CEPH samples. This data was generated as part of the following study: - Population Variation and Genetic Control of Modular Chromatin Architecture in Humans. Cell. 2015 Aug 27;162(5):1039-50. doi: 10.1016/j.cell.2015.08.001. Epub 2015 Aug 20. An additional set of 111 samples from the 1000 Genomes Project (GBR and TSI populations) were also assayed using RNA-seq. This data was generated as part of the following study: - Chromatin 3D interactions mediate genetic effects on regulatory networks.

2016-05-27 | E-MTAB-3656 | biostudies-arrayexpress

Variation and genetic control of chromatin architecture in humans (ChIPseq)

Project description:This data set comprises population (47 samples) measurements of transcription factor DNA binding (PU.1 and RPB2) and histone modification (H3K27ac, H3K4me1 and H3k4me3) levels for a subset of the 1000 Genomes Project CEPH samples. This data was generated as part of the following study: - Population Variation and Genetic Control of Modular Chromatin Architecture in Humans. Cell. 2015 Aug 27;162(5):1039-50. doi: 10.1016/j.cell.2015.08.001. Epub 2015 Aug 20. An additional set of 111 samples from the 1000 Genomes Project (GBR and TSI populations) were also assayed for three histone modifications (H3K27ac, H3K4me1 and H3k4me3). This data was generated as part of the following study: - Chromatin 3D interactions mediate genetic effects on regulatory networks.

2019-03-14 | E-MTAB-3657 | biostudies-arrayexpress

The pancreatic islet MHC-II peptidome identifies key features of autoimmune peptides

Project description:The nature of autoantigens that trigger autoimmune diseases has been much discussed but direct biochemical identification is lacking for most. Addressing this question demands unbiased examination of the self-peptides displayed by a defined autoimmune MHC-II molecule. We have examined the immunopeptidome of the pancreatic islets of the NOD mouse that spontaneously develops autoimmune diabetes based on its MHC-II, the I-Ag7 variant. The relevant peptides that induced early CD4 T cells derived from insulin and C-peptide; these were also found in the MHC-II peptidome of the pancreatic lymph node and spleen. The insulin-derived peptides followed a trajectory from internal processing in beta cells to exocytosis, uptake, and presentation in islets and peripheral sites. Such process not only generated conventional epitopes but also resulted in presentation of post-translationally modified peptides, including deamidated and fused sequences. These analyses reveal the key features of a restricted component in the self-MHC-II peptidome causing autoreactivity.

2020-03-12 | PXD015408 | Pride

Lentinula edodes strain:CS-560

Project description:Lentinula edodes CS-560 Transcriptome - CS-560-R

| PRJNA655104 | ENA

Reanalysis of Pandey lab's draft of the human proteome

Project description:The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides was lacking. To this end, Akhilesh Pandey's lab reported a draft map of the human proteome based on high resolution Fourier transform mass spectrometry-based proteomics technology, which included an in-depth proteomic profiling of 30 histologically normal human samples including 17 adult tissues, 7 fetal tissues and 6 purified primary hematopoietic cells ( http://dx.doi.org/10.1038/nature13302 ). The profiling resulted in identification of proteins encoded by greater than 17,000 genes accounting for ~84% of the total annotated protein-coding genes in humans. This large human proteome catalog (available as an interactive web-based resource at http://www.humanproteomemap.org) complements available human genome and transcriptome data to accelerate biomedical research in health and disease. Pandey's lab and collaborators request that those considering use of this primary dataset for commercial purposes contact pandey@jhmi.edu. The full details of this study can be found in the PRIDE database: www.ebi.ac.uk/pride/archive/projects/PXD000561/. This ArrayExpress entry represents a top level summary of the metadata only which formed the basis of the reanalysis performed by Joyti Choudhary's team ( jc4@sanger.ac.uk ), results of which are presented in the Expression Atlas at EMBL-EBI : http://www.ebi.ac.uk/gxa/experiments/E-PROT-1.

2015-03-10 | E-PROT-1 | biostudies-arrayexpress

CpG island mediated linear and spatial gene partitioning (RNA-seq)

Project description:We reanalyzed published RNA-seq data to study 1) the genomic landscapes near surrounding regions of transcriptional start sites with regard to the gene expression activities and 2) the gene expression change upon transcription factor (MYBL1, ATF4) depletion. Raw data were downloaded from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI) database. FASTQ files were extracted with the SRA Toolkit version 2.5.5 and aligned using STAR 2.4.2 onto the mouse and human genome (mm9 and hg19, respectively). Gene expression was calculated as RPKM values using rpkmforgenes.py (Ramsköld et al., 2009).

2018-02-15 | GSE80793 | GEO

Project description:111

| PRJNA640831 | ENA

CpG island mediated linear and spatial gene partitioning (ChIP-seq)

Project description:In order to elucidate the general rules for gene localization and regulation mediated by CpG islands, we reanalyzed published ChIP-seq data of CXXC domain, H3K9me3, KDM2A, SUV39H1, ATF4, MYBL1, MYOD1, SPI1, and CTCF. Raw data were downloaded from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI) database. FASTQ files were extracted with the SRA Toolkit version 2.5.5 and aligned using Bowtie 2.2.5 onto the mouse and human genome (mm9 and hg19, respectively). For the identification of factor binding sites, model-based analysis for ChIP-seq peak caller (MACS 1.4.2) was used with a p-value cutoff of 1e-5.

2018-02-15 | GSE80791 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data