Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

46 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ScRNA-seq of T cell differentiation in Artificial Thymic Organoid

ABSTRACT: We followed the PSC-ATO protocol as previously described in Montel-Hagen et al. 2019, and differentiated from two iPSC lines, HPSI0114i-kolf_2 (Kolf) and HPSI0514i-fiaj_1 (Fiaj), to single positive T cells. The following include scRNA-seq data from intermediate cells sampled at day -14, day -7 (two samples), day 0 and week 1 of the protocol. For data of later time points (week 3, 5 and 7), please see accession number E-MTAB-11343.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): mixed sample

SUBMITTER: Chenqu Suo

PROVIDER: E-MTAB-12720 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Mapping the developing human immune system across organs - scRNA-seq

Project description:We profiled hematopoietic, lymphoid and peripheral fetal organs to systematically assess the heterogeneity of immune cell populations across human tissues during development. Single-cell suspensions were obtained from fresh tissue. Cells were either DAPI-CD45+ or DAPI-CD45- FACS-isolated cells, or unsorted.

2022-05-12 | E-MTAB-11343 | biostudies-arrayexpress

The exonuclease TREX1 constitutes an innate immune checkpoint limiting cGAS/STING-mediated anti- tumor immunity

Project description:Given that TREX1-deficient tumor cells showed a growth delay in immunocompetent but not immunodeficient hosts, we characterize the consequences of CT26 tumor-intrinsic TREX1 loss on the host immune system by performing single-cell RNA sequencing on intra-tumoral immune cells sorted from control and TREX1 KO CT26 tumors.

2024-03-12 | E-MTAB-13823 | biostudies-arrayexpress

Obesity drives depot-specific vascular remodeling in white adipose tissue

Project description:Obesity-driven pathological expansion of white adipose tissue (WAT) is a key driver of endothelial dysfunction. Contrary to this paradigm, early vascular alterations associated with over nutrition also exacerbate AT dysfunction. To dissect this complex cause and consequence relationship, here we perform a single-cell transcriptomics screen to generate a detailed landscape of endothelial heterogeneity and vascular alterations in murine model of obesity. Given the differences in ontogeny and function of distinct WAT depots, we demarcate key differences in subcutaneous and visceral WAT vasculature. In addition to descriptive taxonomy, we perform in-depth validation and characterization of our in silico data. We identify a sWAT specific fenestrated endothelial cell subtype, which is drastically reduced in obese conditions. This reduction was associated with a decrease in VEGFA expressing perivascular cells. The novel endothelial subtypes provide a basis for future research and new directions for therapeutic interventions.

2023-05-26 | E-MTAB-12855 | biostudies-arrayexpress

Mapping T cell responses to native and neo- islet antigen epitopes in at risk and type 1 diabetes subjects

Project description:Gene expression and T cell receptor profiles from single cells from populations of T cells stimulated with islet autoantigenic peptides. CD4 T cells were stimulated with native (proinsulin, GAD fragments) or neo-antigen epitopes or flu vaccine (Pediacel). Activated cells (identified as CD19- CD3+ CD4+,CD45-RO+ CD95+, CD154+CD69+ CD27+) were FACS-sorted, barcodes for samples were introduced with cell hashing as follows: patient, 1 pool 1 (Hashtag 1); patient 1 pool 2 (Hashtag 2) patient 2 pool 1 (Hashtag 3); patient 2 pool 2 (Hashtag 4) and Pediacel (patient 1 and 2; Hashtag 5). Hashtag info in ADT files, TCR sequences provided in VDJ files.

2021-05-29 | E-MTAB-10323 | biostudies-arrayexpress

CT26 sorted in vivo tumor cells with Trex1 KO

Project description:The DNA exonuclease TREX1 degrades endogenous cytosolic DNA. Cytosolic DNA triggers the cGAS/STING pathway which increases type I interferon. To investigate the physiological significance of TREX1 loss on in vivo tumor growth, we implanted control and TREX1-deficient CT26 tumor cells into immunocompetent BALB/c hosts.Tumor cells were collected 7 days after tumors reached around 200mm3.

2024-03-12 | E-MTAB-13816 | biostudies-arrayexpress

An in vivo neuroimmune organoid model to study human brain environment-dependent microglia phenotypes

Project description:Characterization of human stem cell-derived microglia (hMG) that develop within vascularized human brain organoids under physiological conditions in vivo. We isolated tdT+/CD45+ hMG from five animals and three time points (6, 12 and 24 weeks post transplantation) using Fluorescence-activated cell sorting (FACS), following a strictly controlled ex vivo isolation procedure as previously described (Gosselin et al., 2017) and profiled those cells using single cell RNA sequencing.

2023-05-11 | E-MTAB-11522 | biostudies-arrayexpress

MPS vaccination alters long-term gene expression of antigen-presenting cells in lymph nodes

Project description:Given the importance of sustained antigen presentation in maintenance of lymph node (LN) immune responses, we hypothesized that vaccine antigen availability and antigen-presenting cell (APC) populations may affect LN expansion. Compared to LNs of mice given the full MPS vaccine, LNs of mice given an MPS vaccine without antigen became prominently less enlarged and contracted sooner.To identify potential mediators of this differential, antigen-dependent response, we next focused the analysis of our scRNA-seq dataset on LN APC populations.

2024-04-05 | E-MTAB-13698 | 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

The effect of insulin-like growth factor 1 treatment on cardiac myeloid cells 3 days post-myocardial infarction

Project description:To test the mechanism by which IGF1 is cardioprotective, we performed single cell RNA sequencing on myeloid cells isolated from the heart 3 days after myocardial infarction of mice with and without IGF1 treatment. Myocardial infarction was induced in C57Bl6/J mice by 45 min occlusion of the left anterior descending artery followed by 3 days of reperfusion. Animals of the IGF1 group (n=3) received 40 ng/g mature recombinant IGF1 subcutaneously as bolus at the beginning of reperfusion. In addition, IGF1 (1 µg/g/d) was administered continuously during reperfusion using micro-osmotic pumps (Alzet, 1003D) that were implanted subcutaneously. Control mice received vehicle (0.1% BSA). After 3 days hearts were digested and CD45+CD11b+ cells were isolated using FACS cell sorting. Each sample contained cells containing 1 control and 1 IGF1 treated mouse, labeled with TotalSeq hashtags. 16000 cells were used as input for the single-cell droplet libraries generation for each sample.

2023-12-31 | E-MTAB-11590 | biostudies-arrayexpress

Charting the age-altered thymic epithelial cell differentiation by lineage tracing from a beta 5-t expressing TEC progenitor

Project description:TEC progenitors that express beta 5-t contribute to both the cortical and medullary TEC compartments. Our initial experiments across ageing thymi identified a population of potential progenitor TECs which expanded with age, and appears to be a progenitor population for mTEC. These lineage tracing experiments are designed to chart the altered differentiation and senescence of mTEC progenitors with age.

2020-09-14 | E-MTAB-8737 | 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