Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ScRNA-seq for mEpiSCs (epiblast stem cells) differentiated to posterior primitive streak (PPS) in vitro, in a monolayer

ABSTRACT: EpiSCs established from murine epiblast were differentiated to posterior primitive streak (PPS) and analyzed using scRNA-seq to investigate identity and homogeneity of the resulting population.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Anna Drozd

PROVIDER: E-MTAB-12106 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

scRNA-seq of mouse EpiSCs (epiblast stem cells) differentiated to extraembryonic mesoderm in vitro, in a monolayer

Project description:EpiSCs derived from epiblast of a gastrulating embryo differentiated towards extraembryonic mesoderm to test the efficiency of the differentiation protocol and identity and homogeneity of the resulting cell population.

2022-11-30 | E-MTAB-12107 | biostudies-arrayexpress

Single-cell RNA-seq of tailbuds from control, Pbx1/Pbx2 compound and Pbx1/Pbx2 double-knockout E8.5/E9.0 embryos.

Project description:In vertebrates, body axis elongation is fuelled by bipotent neuromesodermal progenitors (NMPs), which support the development of both spinal cord and paraxial mesoderm (PM). NMPs reside in the caudal lateral epiblast and tailbud, from where they sustain axial elongation. HOX transcription factors have been historically implicated in axial elongation, with their sequential activation playing a fundamental role in timing PM development. PBX1 and PBX2 are obligate anterior HOX cofactors, and therefore they represent prominent candidates for controlling the distinct response to individual HOX factors. To pinpoint the role of PBX proteins in the development of pre-somitic mesoderm, single-cell RNA sequencing (scRNA-seq) was performed on cells isolated from the tailbuds of control, Pbx1/Pbx2 compound (Pbx1/2-com) and Pbx1/Pbx2 double-mutant (Pbx1/2-DKO) embryos at embryonic days 8.5 and 9.0. Single cells from at least three embryos per genotype and stage were FACS-sorted into 384-well capture plates, and scRNA-seq was performed using MARS-seq (Jaitin D.A. et al., Science, 343, 776-779 (2014)). As a spike-in internal control for batch-effect correction, 71 EpiSCs cultivated in vitro were sorted into each plate, together with 311 cells from embryonic tailbuds. Two wells were left empty in each plate, as a no-cell control during data analysis.

2021-07-21 | E-MTAB-9785 | biostudies-arrayexpress

Single-cell RNA-seq of wild-type and Pbx1/Pbx2 double-knockout EpiSCs differentiated in vitro to pre-somitic mesoderm in the first 48 hours of differentiation.

Project description:In vertebrates, body axis elongation is fuelled by bipotent neuromesodermal progenitors (NMPs), which support the development of both spinal cord and paraxial mesoderm (PM). HOX transcription factors have been historically implicated in axial elongation, with their sequential activation playing a fundamental role in timing PM development. PBX1 and PBX2 are obligate anterior HOX cofactors, and therefore they represent prominent candidates for controlling the distinct response to individual HOX factors. To pinpoint the role of PBX proteins in the development of pre-somitic mesoderm (PSM), wild-type (WT) and Pbx1/Pbx2 double-mutant (Pbx1/2-DKO) EpiSCs were differentiated in vitro to PSM. Single cells from different time-points (WT: EpiSCs, 6 hours, 12 hours, 24 hours, 36 hours, 48 hours; Pbx1/2-DKO: 24 hours, 36 hours, 48 hours) were FACS-sorted into 384-well capture plates, and single-cell RNA-sequencing was performed using MARS-seq (Jaitin D.A. et al., Science, 343, 776-779 (2014)). Two wells were left empty in each plate, as a no-cell control during data analysis.

2021-07-21 | E-MTAB-9774 | biostudies-arrayexpress

Single-cell RNA counting at allele- and isoform-resolution using Smart-seq3

Project description:Large-scale sequencing of RNAs from individual cells can reveal patterns of gene, isoform and allelic expression across cell types and states. However, current single-cell RNA-sequencing (scRNA-seq) methods have limited ability to count RNAs at allele- and isoform resolution, and long-read sequencing techniques lack the depth required for large-scale applications across cells. Here, we introduce Smart-seq3 that combines full-length transcriptome coverage with a 5’ unique molecular identifier (UMI) RNA counting strategy that enabled in silico reconstruction of thousands of RNA molecules per cell. Importantly, a large portion of counted and reconstructed RNA molecules could be directly assigned to specific isoforms and allelic origin, and we identified significant transcript isoform regulation in mouse strains and human cell types. Moreover, Smart-seq3 showed a dramatic increase in sensitivity and typically detected thousands more genes per cell than Smart-seq2. Altogether, we developed a short-read sequencing strategy for single-cell RNA counting at isoform and allele-resolution applicable to large-scale characterization of cell types and states across tissues and organisms.

2020-04-14 | E-MTAB-8735 | biostudies-arrayexpress

Single-cell RNA-sequencing of spinal cord ependymal cells from FOXJ1-EGFP mice

Project description:The spinal cord neural stem cell potential is contained within the ependymal cells lining the central canal. Ependymal cells are, however, heterogeneous and we know little about what this reflects. To gain new insights into ependymal cell heterogeneity, we microdissected the ependymal cell layer from the thoracic spinal cord of 4 FOXJ1-EGFP transgenic mice (2.5-to-3-month old). After after dissociating the tissue into a cell suspension, we sorted single GFP-positive ependymal cells into lysis plates. cDNA synthesis was performed using Smart-seq2 technology.

2022-12-13 | E-MTAB-11563 | biostudies-arrayexpress

scATAC-seq of mouse Plasmodium-specific CD4+ T cells

Project description:Plasmodium-specific CD4+ T cells from mice infected with Plasmodium chabaudi chabaudi AS parasites were recovered at Days 0, 4, 7, and 32 to undergo processing and to generate scATAC-seq dataset. At Day 7, CXCR5+ and CXCR6+ cells were recovered separately. At Day 32, mice were administered with either saline or artesunate (intermittent artesunate therapy - IAT). scATAC-seq dataset was analysed to investigate epigenomic landscapes of CD4+ T cells from effector to memory states.

2020-10-14 | E-MTAB-9402 | biostudies-arrayexpress

RNA-seq of wild-type and PGR (progesterone receptor) knockout pluripotent mouse EpiSCs (epiblast stem cells) and differentiated samples derived from these cell lines (primitive streak and mesoderm)

Project description:EpiSCs (epiblast stem cells) are murine pluripotent stem cells derived from the epiblast of a post-implantation embryo. These cells are primed to differentiate towards embryonic germ layers and are a useful model to study these early developmental events. PGR (progesterone receptor) is a nuclear receptor described mainly in the context of fertility and breast cancer. We noticed that it is also a TF that is expressed in primed EpiSCs, but not in naive mESCs and is further upregulated during mesoderm specification. We hypothesized that it is involved in differentiation to primitive streak and mesoderm progenitors. To test this hypothesis we generated EpiSCs with a genetic knockout of PGR using CRISPR-Cas9-mediated knock-in of an antibiotic resistance cassette. Differentiation of the wild-type and knockout cells and comparison of the different cell types allowed us to conclude that PGR is important for acquiring extraembryonic mesoderm fate and modulates cardiac differentiation, specifically it ensures that correct pools of FHF (first heart field) and SHF (second heart field) are being produced. Our study sheds light on previously unappreciated role of PGR in early embryonic development.

2022-11-30 | E-MTAB-12104 | biostudies-arrayexpress

Single-cell RNA-sequencing of mouse thymic epithelial cells across the first year of life

Project description:The thymus shapes the T cell receptor repertoire, and is one of the first organs to rapidly age, with gross changes in cellularity and architecture. To resolve the nature of these changes we used SMART-Seq2 on FACS purified thymic epithelial cells (TEC) across the first year of mouse life. We sorted 4 TEC populations in each of 5 mice at each age (1 week, 4 weeks, 16 weeks, 32 weeks and 52 weeks old).

2020-09-14 | E-MTAB-8560 | biostudies-arrayexpress

ScRNA-seq analysis of naive, germinal center and memory B cells of mice immunized with homologous and heterologous prime:boost combinations of whole-cell pertussis or acellular pertussis vaccines

Project description:Since the introduction of new generation pertussis vaccines, resurgence of pertussis is observed in many developed countries. Former whole-cell pertussis vaccines (wP) are able to protect against disease and transmission but have been replaced in several industrialized countries because of their reactogenicity and adverse effects. Current acellular pertussis vaccines (aP), made of purified proteins of Bordetella pertussis, are efficient at preventing disease but fail to induce long-term protection from infection. While the systemic and mucosal T cell immunity induced by the two types of vaccines has been well described, much less is known concerning B cell responses. Taking advantage of an inducible AID-Cre-EYFP fate-mapping mouse model, we sorted and analyzed by scRNAseq the transcriptomic profiles of memory B cells after a combination of prime:boost with the two classes of vaccines. B220+EYFP+GL7-PNA- memory B cells from the draining lymph nodes (dLNs) of tamoxifen-fed mice were FACS sorted 7 weeks after boost, alongside with B220+EYFP+GL7+PNA+ germinal center (GC) B cells and B220+GL7-PNA-EYFP-IgD+ naive B cells as a control population for the unsupervised clustering analysis. Single-cell mRNA sequencing was performed according to an adapted version of the SORT-seq protocol (Muraro et al., 2016, PMID: 27693023, with primers described in van den Brink et al. 2017), with cDNA libraries generation, sequencing and reads alignment performed at Single Cell Discoveries (Utrecht, Netherlands).

2022-09-12 | E-MTAB-12156 | biostudies-arrayexpress

Impact of Hells loss-of-function on DNA methylation in B cells during humoral immune responses: kinetic comparison of Mb1-Hells knockout and control mice by single-cell RNA sequencing

Project description:We are interested in deciphering the mechanism by which DNA methylation in late B cell differentiation affects humoral immune response. We chose to study a very rare immunodeficiency called ICF type 4, where a point mutation in a gene encoding the protein HELLS causes a lack of both circulating antibodies and memory B cells in human. HELLS is a chromatin remodeler, that allows for DNA methylation to occur. Using a Hells conditional knock-out in B cells, we measured the kinetics of the immune B cell response, following immunization with NP-CGG, and show a lack of memory and plasma cells accompanied by a defect in germinal center maintenance, but not by its formation. Single cell RNAseq of cell sorted naive, germinal center B cells and memory B cells at day 7 and day 14 post NP-immunization helped us better characterize the phenotype.

2023-07-25 | E-MTAB-12499 | 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