Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell RNA-seq of Endometrial Superficial biopsies and full depth uterine tissue from organ donors

ABSTRACT: We performed single-cell RNA-sequencing to create a cell census of the human endometrium, which is the mucosal lining of the uterus that undergoes dynamic changes throughout the menstrual cycle. We integrated cells that were obtained from 3 superficial biopsies to selected samples that originated from 2 organ donors; this allowed a better representation of cell type diversity found within the full depth of the endometrium.

INSTRUMENT(S): Illumina NovaSeq 6000, Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Louis-Francois Handfield

PROVIDER: E-MTAB-10287 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single-cell RNA-seq of Endometrial organoids treated with NOTCH or WNT inhibitors in a time course of Estrogen and Progesterone stimulation

Project description:We performed single-cell RNA-sequencing of 3D endometrial organoid cultures in order to dissect the signaling pathways that determine cell fate of epithelial lineages. Every time course was obtained in a background that either included or did not include ovarian hormones stimulation, which emulates dynamic regulations associated with the menstrual cycle. These inductions show that in vitro downregulation of WNT or NOTCH pathways increases the differentiation efficiency along the secretory and ciliated lineages, respectively.

2021-07-21 | E-MTAB-10283 | biostudies-arrayexpress

Single-cell RNA seq of mouse proximal small intestine at E16.5

Project description:Epcam-positive cells from fetal intestinal epithelium were FACS sorted and processed using 10X genomics to characterise the differentiation of fetal intestinal cells at E16.5.

2019-05-15 | E-MTAB-7660 | biostudies-arrayexpress

Human fetal liver CITE-seq data

Project description:In this study we used single cell multi-omics profiling to create an atlas of the human YS to gain insights into its haematopoietic, metabolic and nutritive functions during early embryonic development. This contains fetal liver CITE-seq (surface protein and cytosolic RNA content) data from six biological replicates. Pooled lanes were demultiplexed using SoupOrCell (for alignment and demultiplexing software and version numbers, please see accompanying manuscript and protocols within this accession). Raw count files provided are directly as output by alignment software, without any quality control applied. Quality control is described in accompanying manuscript methods. Metadata by barcode are provided as supplementary tables in accompanying manuscript.

2022-12-08 | E-MTAB-11613 | biostudies-arrayexpress

Human embryonic liver CITE-seq data

Project description:In this study we used single cell multi-omics profiling to create an atlas of the human YS to gain insights into its haematopoietic, metabolic and nutritive functions during early embryonic development. This contains embryonic liver CITE-seq (surface protein and cytosolic RNA content) data from three biological replicates. Pooled lanes were demultiplexed using SoupOrCell (for alignment and demultiplexing software and version numbers, please see accompanying manuscript and protocols within this accession). Raw count files provided are directly as output by alignment software, without any quality control applied. Quality control is described in accompanying manuscript methods. Metadata by barcode are provided as supplementary tables in accompanying manuscript.

2022-12-08 | E-MTAB-11618 | biostudies-arrayexpress

Human embryonic yolk sac CITE-seq data

Project description:In this study we used single cell multi-omics profiling to create an atlas of the human YS to gain insights into its haematopoietic, metabolic and nutritive functions during early embryonic development. This contains CITE-seq data (surface protein and cytosolic RNA content) data from two biological replicates. Pooled lanes were demultiplexed using SoupOrCell (for alignment and demultiplexing software and version numbers, please see accompanying manuscript and protocols within this accession). Raw count files provided are directly as output by alignment software, without any quality control applied. Quality control is described in accompanying manuscript methods. Metadata by barcode are provided as supplementary tables in accompanying manuscript.

2022-12-08 | E-MTAB-11549 | biostudies-arrayexpress

Spatial transcriptomics of superficial endometrial biopsies from women in reproductive age

Project description:The study profiles endometrial samples from donors in reproductive age with and without endometriosis collected during natural cycles. Samples where profiled with Visium Spatial transcriptomics using 10x technology (v1 3').

2024-05-13 | E-MTAB-14058 | biostudies-arrayexpress

Spatial transcriptomics of human implantation sites, placenta and decidua

Project description:These samples are part of a study to provide a spatially resolved single-cell multiomics map of human trophoblast differentiation in early pregnancy. Here we profiled with 10x Visium Spatial transcriptomics of the entire maternal-fetal interface including the myometrium, allowing us to resolve the full trajectory of trophoblast differentiation.

2023-02-03 | E-MTAB-12698 | biostudies-arrayexpress

multiomic snRNAseq/snATACseq of first and second-trimester human gonads

Project description:Comprehensive map of first- and second-trimester gonadal development in humans using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays, and imaging.

2022-05-12 | E-MTAB-11708 | biostudies-arrayexpress

Primordial germ cell like cell competent populations

Project description:We sequenced human embryonic stem cells (hESCs), pre-mesendoderm cells (PreME) that acquire transient competence for PGCLC specification and cells at the mesendoderm (ME) stage when they are not longer PGC-competent.

2022-01-21 | E-MTAB-11135 | biostudies-arrayexpress

scRNAseq of immune cells of patients with chronic graft-versus-host disease

Project description:In this study, we investigated somatic mutations in T cells in patients with various hematological disorders. To analyze immune cell phenotypes with somatic mutations, we performed scRNA+TCRab sequencing from 9 patients with chronic GVHD and clonal expansions of CD4+ or CD8+ T cells based on T cell receptor sequencing. CD45+ PBMCs (lymphocytes and monocytes) were sorted with BD Influx cell sorter and subjected to sequencing with Chromium VDJ and Gene Expression platform (v1.1, 10X Genomics). Sequencing was performed with Novaseq 6000 (Illumina). The immune cell phenotypes were compared to healthy controls processed in the same laboratory (accession number E-MTAB-11170). Due to data privacy concerns, the raw sequencing data is in the European Genome-Phenome Archive (EGA) under accession code [xxxx] and can be requested through the EGA Data Access Committee.

2024-04-10 | E-MTAB-13419 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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