Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

27 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ScATAC-seq of fetal thymus

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Mirjana Efremova

PROVIDER: E-MTAB-9828 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

Multiome scRNA- and scATAC-seq of healthy and trisomy 21 (Down's syndrome) foetal liver

Project description:Here, we performed multiome sequencing (snRNA-seq + snATAC-seq) of human fetal liver samples from 3 trisomy 21 (Ts21) and 3 healthy foetuses (median age 14 post-conception weeks). The data set is composed of approximately 60,000 CD45+ foetal liver cells.

2024-07-17 | E-MTAB-13070 | 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

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

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

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

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

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

2022-05-03 | E-MTAB-10589 | biostudies-arrayexpress

Genotyping by array: Human Developmental Biology Resource (HDBR) expression resource of prenatal human brain development-SNP data

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) and HDBR expression resource- SNP data (E-MTAB-4843, this submission). 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; 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 embryo/fetus have the same ID number (e.g. RNAseq datasets HDBR251-HDBR254 are from different tissues from embryo number 1406). The embryo/fetus ID number is recorded in the âindividualâ 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 individual embryo or fetus 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. For the specimens in wax blocks, the SNP genotype data was generated from DNA from either skin or placenta. The tissues present in the corresponding wax block(s) are given in the biosource type column.

2016-10-12 | E-MTAB-4843 | biostudies-arrayexpress

Placental infection single-cell and single-nuclei maps

Project description:This resource comprises a single-cell multi-lineage map of first trimester infected placental cells. We have included data from both uninfected cells and cells infected with three pathogens known to cause maternal and fetal disorders: Plasmodium falciparum, Listeria monocytogenes, and Toxoplasma gondii. We also generated single-nuclei map of infected trophoblasts and their corresponding controls. Furthermore, we created a single-nuclei reference dataset containing information from uninfected primary placental organoids as well as organoids infected with P. falciparum. Additionally, we conducted sequencing at a single-cell level for P. falciparum parasites that were bound to the placenta (pf_b), parasites unbound to the placenta (pf_nb), and parasites that were cultured in vitro (pf_iv).

2024-03-01 | E-MTAB-12795 | 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