Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell RNA sequencing of iPSC and Human dermal fibroblasts

ABSTRACT: single cell RNA sequencing of iPSC and Human dermal fibroblasts using 10x Genomics with 3-prime, 5-prime poly(dT) primer, and 5-prime random primer. For comparison in gene, ncRNA and enhancer detection.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Jonathan Moody

PROVIDER: E-MTAB-10385 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single cell five-prime end sequencing of PBMC - resting and stimulated

Project description:Single cell five-prime end sequencing of PBMC - resting and stimulated. Used to asses the five-prime sequencing method in the detection of cis-regulatory elements using SCAFE (see publication)

2021-04-28 | E-MTAB-10378 | biostudies-arrayexpress

Single cell ATAC-seq of human peripheral blood mononuclear cells under resting and stimulated conditions

Project description:Single cell ATAC-seq of PBMC - resting and stimulated. Used for comparison to asses the capabilies of the five-prime sequencing method in the detection of cis-regulatory elements using SCAFE (see publication).

2021-04-13 | E-MTAB-10382 | biostudies-arrayexpress

Single-cell RNA-Sequencing of testis tissue from 3 mouse species and their immediate crosses

Project description:We performed an inter-species comparison of murine spermatogenesis using the inbred strains C57B6J, CAST/EiJ and CAROLI/EiJ to investigate the cell type-specific evolution of gene expression levels among closely related species. We also used F1 crosses of C57B6J and CAST/EiJ to investigate context-specific regulatory effects on gene expression in cis and trans by measuring allele-specific expression (Goncalves et al. 2012; Wittkopp et al. 2021). To this end, single-cell RNA-Sequencing data was generated from dissociated testicular tissue in each mouse strain using the 10x Genomics scRNA-Seq platform.

2023-12-11 | E-MTAB-11602 | biostudies-arrayexpress

Single-cell transcriptional analysis reveals ILC-like cells in zebrafish

Project description:Transcriptome data from zebrafish single cells from guts from either from Tg(lck:EGFP) rag1-/-mutant or wild-type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish, per each condition (i.e. zebrafish intraperitoneally injected with PBS, lyophilised Anisakis simplex or inactivated Vibrio anguillarum), were used to collect the total of 12,000 lck+ cells (4000 per zebrafish) for 10x experiment.

2018-11-16 | E-MTAB-7159 | biostudies-arrayexpress

Evading immune evasion via reprograming of the tumor microenvironment by radiotherapy and simultaneous targeting of TGF-β/PD-L1

Project description:Single cell transcriptome showed TGF-β expression is confined to PD-L1+ endothelium and M2 /lipofibroblast-like cells. Hence, superior effects of BA could be attributed to its ability to trap TGF-β to relevant PD-L1+ compartments. Mice were irradiated (photon) and one group of mice was treated with Bintrafusp. Lungs were subsequently dissociated and processed with the 10x genomics 3 prime v2 kit.

2021-08-10 | E-MTAB-10633 | biostudies-arrayexpress

scRNAseq of heterozygous HNF1B-mutant vs non-mutant kidney organoids derived from human embryonic stem cells

Project description:Human embryonic stem cell (hESC) line Man-13 was edited by CRISPR resulting in a hESC line carrying a heterozygous frameshift mutation with a premature stop codon in exon-1 of the HNF1B gene ([p.Val61Argfs*18]), functionally equivalent to a heterozygous whole-gene deletion. Kidney organoids were then created by differentiation (as per Takasato et al, 2015; Bantounas et al, 2018; Bantounas et al 2021) of this line and an isogenic non-mutant control line. Single-cell RNAseq (scRNAseq) was then performed on day-25 of differentiation to identify transcriptomic differences, as well as differences in identity and numbers of the cell populations comprising the organoids, with the aim of mechanistically explaining developmental aberrations observed in patients with mutations in this gene.

2024-04-30 | E-MTAB-13500 | biostudies-arrayexpress

scRNA-seq of Human midbrain organoids differentiated from WTSIi018-B-1 (healthy) and EDi001-B (Parkinson's Disease) iPSCs

Project description:Day 49 organoid differentiation of midbrain organoids

2023-01-01 | E-MTAB-12339 | biostudies-arrayexpress

Single-cell RNA sequencing of mouse primary B cells to investigate subpopulation markers

Project description:The project aims at linking functionality to metabolic fluxes of mouse primary B cells, potentially correlating antibody secretion rates with metabolic differences in subpopulations of B cells. In previous experiments, subpopulations of primary B cells with different phenotypes were observed. Therefore, the next step is to further characterize these subpopulations of B cells via single-cell RNA sequencing so that we gain insight about cell characteristics and individual gene markers, and their potential biological role. Our hypothesis is that these cells present different expression profiles of key genes and/or are relevant in different immune-related pathways.

2023-11-20 | E-MTAB-13205 | 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

Haematopoietic stem and progenitor cells are present in healthy gingiva tissue

Project description:Haematopoietic stem cells reside in the bone marrow where they generate the effector cells that drive immune responses. However, in response to inflammation some haematopoietic stem and progenitor cells (HSPC) are recruited to tissue sites and undergo extramedullary haematopoiesis. Contrasting this paradigm here we show, with single cell sequencing, residence and differentiation of HSPC in healthy gingiva, a key oral barrier, in the absence of overt inflammation.

2021-02-23 | E-MTAB-10050 | 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