Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

3a2d18fe-577e-46c5-a4a9-a5677ca88921 - samples

ABSTRACT: This dataset includes 1,359 paired-end shotgun metagenomics samples from 946 healthy donors of the Milieu IntÃƒÂ©rieur cohort. 413 of the donors provided two samples (V1 and V2).

PROVIDER: EGAD00001006554 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

LabExMI_SNP_genotyping

Project description:Genotype data for 5,699,237 genotyped and imputed SNPs in the 816 healthy donors of the Milieu IntÃƒÂ©rieur cohort

| EGAD00010001489 | EGA

Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression

Project description:Purpose: Single cell sequencing has advanced our understanding of kidney biology. The goals of this study are to compare single nucleus RNA (snRNA-seq) and single nucleus assay for transposase accessible chromatin sequencing (snATAC-seq) from healthy control donors and donors with type 2 diabetic kidney disease to identify altered signaling pathways and chromatin accessibility patterns observed in diabetic kidney disease. Methods: Nuclear dissociation of human kidney cortex samples was performed on samples obtained from patients undergoing tumor nephrectromy or deceased organ donors. snRNA-seq and snATAC-seq libraries were prepared using 10X Genomics kits according to manufacturers instructions. For this study, two healthy control libraries from one donor were prepared with the following chemistries (1 - single cell 3-prime v3, 1 - single cell ATAC v1) and nine DKD libraries from seven donors were prepared with the following chemistries (2 - single cell 5-prime v2 paired-end, 7 - single cell ATAC v1). Raw data for three healthy control and three DKD snRNA-seq libraries sequenced with single nucleus 5-prime R2 only can be found in GSE13188213. Raw data for two healthy control snRNA-seq sequenced with single nucleus 5-prime paired-end and five snATAC-seq single nucleus ATAC v1 libraries can be found in GSE151302. snRNA-seq and snATAC-seq libraries from these earlier studies were recounted with cellranger (v4.0) or cellranger-atac (v2.0) to provide consistency across processed data files.

2022-07-28 | GSE195460 | GEO

Vaginal secretory proteome dynamically changes across the early and mid-trimesters of pregnancy

Project description:This study investigates the dynamic alterations in high vaginal fluid (HVF) proteome and its correlation with physiological changes during progression of term pregnancy. The HVF samples were collected at three time points as defined as V1 (6-12 weeks), V2 (18-20 weeks) and V3 (26-28 weeks) and SWATH-MS strategy were applied to profile changes in protein expression at early and middle stage of pregnancy. Using in-house generated HVF-specific protein library, 61 proteins (>1.5 fold at V2/V1 or V3/V1, q-value <0.05) changed as a function of gestational age. The stage-specific expression pattern of these proteins was mainly associated with the biology of cervical remolding, fetal development and microbial defense.

2021-01-28 | PXD021811 | Pride

Vaginal secretory proteome dynamically changes across the early and mid-trimesters of pregnancy

2021-01-29 | PXD014846 | Pride

SNP array data for the Milieu IntÃƒÂ©rieur cohort

Project description:The Milieu IntÃƒÂ©rieur Consortium aims at identifying the environmental and genetic factors driving variation in innate and adaptive immune systems among healthy individuals. In the last four years, we combined standardized flow cytometric analysis of blood leukocytes, transcriptional profiles of whole blood after immune stimulation and genome-wide DNA genotyping in 1,000 healthy, unrelated donors of western European ancestry, to show that age, sex, as well as persistent infections and smoking, are the most important drivers of inter-individual differences in blood cell composition and transcriptional response to pathogens. The EGAS00001002460 study includes genotype data for 5,699,237 genotyped and imputed SNPs in the 816 healthy donors of the Milieu IntÃƒÂ©rieur cohort. Note that 184 of the 1,000 initial donors did not agree to share their data online.

| EGAS00001002460 | EGA

Pancreatic Tumor vs Various Tissue Normals

Project description:Pancreatic Tumor samples from biopsy collected at different stages along with normal tissue samples from various organ sites including commercial normals arrayed on 2channel Agilent 60mer Oligo arrays (human v1 & v2), median normalized for cross comparison. Some normal samples temporarily removed to public due to Intelectual property conflict. Keywords: Pancreatic tumor comparison to normals for multimetric study

2008-09-15 | GSE11838 | GEO

DPHL v2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins

Project description:we generated DPHL v2 from 1608 DDA-MS data acquired using Orbitrap mass spectrometers. The data included 586 DDA-MS newly acquired from 17 tissue types, while 1022 files were derived from DPHL v1. DPHL v2 thus comprises data from 24 sample types, including several cancer types . We generated four variants of DPHL v2 to include semi-tryptic peptides and protein isoforms.

2023-01-18 | PXD039313 |

Modular repertoire analyses identify dynamic type I and type II interferon transcriptional signatures in adult SLE patients

Project description:Gene expression profiling (compared to healthy controls) to identify patients with active SLE disease and patients with quiescent disease 157 “SLE” and 20 “Healthy controls of SLE were followed up for up to 3 years. Clinical assessment, current treatment, laboratory results and SLEDAI score were collected at each visit (V1, V2...). SLE patients are compared to control groups.

2014-04-01 | E-GEOD-49454 | biostudies-arrayexpress

RNA-seq analysis of resting and inflamed human neutrophils

Project description:This study includes RNA-seq profiles of neutrophils from healthy donors and patients with inflammatory arthritis.

2022-02-19 | GSE193117 | GEO

Single cell RNA sequencing of cells isolated from the intestinal crypts of mice bearing epithelial cell-specific Ptger4 ablation (Drop-seq)

Project description:Crypts isolated from the small intestine of mice bearing epithelial cell-specific ablation of the Ptger4 gene (VillinCrePtger4flox, "V") and normal littermate control mice (Ptger4flox, "F") were dissociated into single cell suspensions and subjected to the Drop-seq protocol. N = 2 mice per genotype were independently processed as biological replicates (V1, V2 and F1, F2). A total of three Drop-seq collections (samples) were processed for each genotype, two from the first biological replicate (V1A, V1B, F1A, F1B) and one from the second biological replicate (V2, F2).

2019-12-21 | GSE142418 | 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