Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatial transcriptomics (Visium) of first and second-trimester human gonads

ABSTRACT: 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.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Luz Garcia-Alonso

PROVIDER: E-MTAB-10589 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Single-cell roadmap of human gonadal development.

Garcia-Alonso Luz L Lorenzi Valentina V Mazzeo Cecilia Icoresi CI Alves-Lopes João Pedro JP Roberts Kenny K Sancho-Serra Carmen C Engelbert Justin J Marečková Magda M Gruhn Wolfram H WH Botting Rachel A RA Li Tong T Crespo Berta B van Dongen Stijn S Kiselev Vladimir Yu VY Prigmore Elena E Herbert Mary M Moffett Ashley A Chédotal Alain A Bayraktar Omer Ali OA Surani Azim A Haniffa Muzlifah M Vento-Tormo Roser R

Nature 20220706 7919

Gonadal development is a complex process that involves sex determination followed by divergent maturation into either testes or ovaries<sup>1</sup>. Historically, limited tissue accessibility, a lack of reliable in vitro models and critical differences between humans and mice have hampered our knowledge of human gonadogenesis, despite its importance in gonadal conditions and infertility. Here, we generated a comprehensive map of first- and second-trimester human gonads using a combination of sin ...[more]

PMID: 35794482

Similar Datasets

scRNA-seq of first and second trimester human gonads - 10x dataset

Project description:scRNA-seq of first and second trimester human gonads

2022-06-30 | E-MTAB-10551 | biostudies-arrayexpress

scATAC-seq 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.

2024-02-05 | E-MTAB-10570 | biostudies-arrayexpress

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

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

spatial transcriptomics (10x Visium) of first and second trimester human reproductive tract

Project description:spatial transcriptomics by means of 10x Visium of first and second trimester human reproductive tract (including female and male internal and external genitalia)

2025-08-06 | E-MTAB-15471 | 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

Spatial transcriptomics (Visium, 10x Genomics) data for human Idiopathic Pulmonary Fibrosis (IPF) and control lung tissue

Project description:Visium (10x Genomics) spatially resolved transcriptomics data generated from normal and Idiopathic Pulmonary Fibrosis (IPF) lung parenchyma tissues collected from human donors. The fresh-frozen tissues that were analyzed were from four healthy control (HC) subjects and from four IPF patients. For each IPF patient, three different tissues were selected representing areas of mild (“B1”), moderate (“B2\") or severe (“B3”) fibrosis within the same donor, as determined by histological inspection of Hematoxylin and Eosin (H&E)-stained samples. Data from a total of 25 tissue sections, from 16 unique lung tissue blocks. The lung tissues were collected post-mortem (HC donors) or during lung transplant/resection (IPF patients) after obtaining informed consent. The study protocols were approved by the local human research ethics committee (HC: Lund, permit number Dnr 2016/317; IPF: Gothenburg, permit number 1026-15) and the samples are anonymized and cannot/should not be traced back to individual donors.

2024-05-28 | E-MTAB-14121 | biostudies-arrayexpress

scRNA-seq of human fetal thymus

Project description:To investigate the gene regulatory mechanisms driving T cell development, we generated single-cell transcriptomics and chromatin accessibility data from a human fetal thymus sample at 10 weeks of gestation.

2021-11-30 | E-MTAB-9840 | biostudies-arrayexpress

Human Developmental Biology Resource (HDBR) expression resource-RNAseq

Project description:The Human Developmental Biology Resource (HDBR) expression resource is a new resource for studying prenatal human brain development. It consists of two parts which have been uploaded as two submissions: HDBR expression resource- RNAseq (E-MTAB-4840, this submission) and HDBR expression resource- SNP data (E-MTAB-4843). It is unique in the age range (4 post conception weeks [PCW] to 17PCW) and number of brains studied, particularly those under 8PCW. It is also unique in that both the large-scale data sets and the corresponding RNA and DNA samples are available, the latter via the MRC-Wellcome Trust Human Developmental Biology Resource (HDBR; http://www.hdbr.org). There are 628 RNA-seq datasets from different regions of the brains studied. The number of regions depends on the stage and size of the sample and/or the tissue available. Embryos (4-8PCW) have been staged using a modified Carnegie staging system, details can be found at http://database.hudsen.eu/. All the RNAseq datasets from the same brain have the same embryo/fetus number (e.g. RNAseq datasets HDBR251-HDBR254 are from different tissues from embryo number 1406). The embryo/fetus ID number is recorded in the individual column. The majority of the brains studied are between 4 and 12PCW. During this time the major brain regions are established and there are the early stages of cortex development. DNA was prepared from all the tissues used for RNA-seq analysis and SNP genotype data generated from one tissue from each brain. RNA-seq data and SNP-data from the same tissue and brain have the same name (e.g. HDBR469). There are also SNP genotype data from 229 additional specimens in paraffin wax blocks available for individual gene expression studies. These data are in the accompanying HDBR expression resource- SNP data (E-MTAB-4843).

2016-10-12 | E-MTAB-4840 | biostudies-arrayexpress

Single cell RNA sequencing of healthy and trisomy 21 (Down's syndrome) foetal liver and foetal bone marrow

Project description:Here, we performed single cell RNA sequencing (scRNA-seq) of human fetal liver and bone marrow tissue samples from 15 trisomy 21 (Ts21) and 3 healthy foetuses (median age 14 post-conception weeks). The data set is composed of approximately 1.1 million cells from three different populations: CD235- (niche and haematopoietic cells depleted of erythrocytes), CD34+/Lin- (haematopoietic progenitors), and CD45+ (all haematopoietic cells).

2024-07-22 | E-MTAB-13067 | 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

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