Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

52 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell analysis of emergent haematopoiesis in the human fetal bone marrow (10X)

ABSTRACT: Haematopoeisis emerges in the human fetal bone marrow (BM) at around 12 post conception weeks. This constitutes the second wave of definitive haematopoiesis following on from the first wave in fetal liver from around 6 post conception weeks. The BM emerges as the dominant site of haematopoiesis, responsible for lifelong blood and immune cell production. Yet, little is known about how the composition of the fetal BM, the microenvironment permissive to establishing haematopoiesis and the interplay with other sites of fetal haematopoiesis in fetal health or disease. Herein we utilise single cell RNA sequencing to describe fetal haematopoeisis throughout gestation and better understand the development of the human immune system.

INSTRUMENT(S): 10x Chromium Controller, Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Muzlifah Haniffa

PROVIDER: E-MTAB-9389 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single cell antigen receptor analysis reveals lymphocyte developmental origins

Project description:To test the impact of nonsense-mediated decay (NMD) on BCR/TCR RNA sequences, we treated peripheral blood mononuclear cells (PBMCs) with cycloheximide to block NMD and analyzed treated and untreated cells by scRNA-seq with scVDJ-seq.

2023-02-28 | E-MTAB-12524 | biostudies-arrayexpress

Single cell CITE-seq and VDJ sequencing of epidermal and blood T cells

Project description:The aim of the experiment was to investigate the clonal relationship between CD8+ T cell subsets of donor matched blood with epidermal CD8+ T cells. Abdominal skin (n=8) was separated into dermis and epidermis, followed by epidermal skin and PBMC isolation. Single CD8+ T cells (n=6) and CD3+ T cells (n=2) were FACS sorted, processed with the 5’ 10x Genomics workflow and sequenced at NGI Sweden.

2023-06-12 | E-MTAB-12839 | biostudies-arrayexpress

Single-cell RNA and BCR sequencing of naive B cells cultured in IgG class-switching polarising conditions

Project description:Naive B cells (CD27-IgD+) were obtained from 3 healthy controls and cultured in vitro under anti-IgM, CD40L and IFN-gamma to polarise class-switching towards IgG isotypes. Single-cell RNA and BCR sequencing libraries were prepared at Day 0 (before addition of stimuli), Day 3 and Day 6 of the cell culture time-course. This is intended as a dataset to validate a new computational method sciCSR in enumerating productive and sterile immunoglobulin transcripts as indicators of B cell class switching and maturation dynamics.

2023-07-01 | E-MTAB-13050 | biostudies-arrayexpress

Single cell analysis of emergent haematopoiesis in the human fetal bone marrow (SS2)

Project description:Haematopoeisis emerges in the human fetal bone marrow (BM) at around 12 post conception weeks. This constitutes the second wave of definitive haematopoiesis following on from the first wave in fetal liver from around 6 post conception weeks. The BM emerges as the dominant site of haematopoiesis, responsible for lifelong blood and immune cell production. Yet, little is known about how the composition of the fetal BM, the microenvironment permissive to establishing haematopoiesis and the interplay with other sites of fetal haematopoiesis in fetal health or disease. Herein we utilise single cell RNA sequencing to describe fetal haematopoeisis throughout gestation and better understand the development of the human immune system.

2021-07-15 | E-MTAB-9801 | 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

Single cell CITE-seq and VDJ sequencing of CD8+ central memory blood T cells (TCM) and their in-vivo matured tissue-resident memory-like T cells (TRM)

Project description:The aim of the experiment was to understand the clonal relationship between CD8+ central memory blood T cells (TCM) and the in-vivo matured TCM tissue-resident memory-like T cells (TRM) on day 14. TCM were FACS sorted from human PBMCs (n=5). Half of the cells were processed on day 1 and half of the cells of each donor were matured into TRM with anti-CD3, IL-15 and TGF beta for 14 days. Both day 1 TCM and matured day 14 TRM-like cells were further processed using the 5´10X genomics workflow.

2023-06-12 | E-MTAB-12840 | biostudies-arrayexpress

A high-resolution single-cell multiomic atlas of the human fetal lung - scRNA / GEX / VDJ

Project description:We obtained human embryonic and fetal lungs from 5-22 pcw for scRNAseq and scATACseq analysis. To focus on epithelial differentiation and region specialization, we deeply sampled 15, 18, 20 and 22 pcw lungs and separated proximal and distal regions while leaving lungs at 5, 6, 9 and 11 pcw intact. These cell samples (except for one at 6pcw) were split and processed for both scRNAseq and scATACseq.

2022-01-27 | E-MTAB-11278 | 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

Single cell analysis of emergent haematopoiesis in the human fetal bone marrow (10X)

Project description:Haematopoeisis emerges in the human fetal bone marrow (BM) at around 12 post conception weeks. This constitutes the second wave of definitive haematopoiesis following on from the first wave in fetal liver from around 6 post conception weeks. The BM emerges as the dominant site of haematopoiesis, responsible for lifelong blood and immune cell production. Yet, little is known about how the composition of the fetal BM, the microenvironment permissive to establishing haematopoiesis and the interplay with other sites of fetal haematopoiesis in fetal health or disease. Herein we utilise single cell RNA sequencing and surface protein characterisation using CITE-seq technology to describe fetal haematopoeisis throughout gestation and better understand the development of the human immune system.

2021-07-15 | E-MTAB-10042 | biostudies-arrayexpress

Somatic mutations in lymphocytes in patients with immune-mediated aplastic anemia

Project description:In this study, we investigated somatic mutations of CD4+ and CD8+ T cells in patients with immune-mediated aplastic anemia (AA). To understand the role of mutations, we performed single-cell level analysis of 6 longitudinal samples of 2 AA patients carrying STAT3 or KRAS and other mutations in CD8+ T cells. The analysis was performed using V(D)J and 5' gene expression platform (10X Genomics). STAT3 mutated clone was clearly distinguishable from other CD8+ T cells and showed a cytotoxic phenotype, attenuated by successful immunosuppressive treatment. Our results suggest that somatic mutations in T cells can alter T cell phenotype warranting further investigation of their role in the pathogenesis of immune-mediated AA.

2021-03-24 | E-MTAB-9969 | 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