Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell RNA-seq of motor neuron progenitors differentiated from mouse embryonic stem cell line HM1 by treatment with RA and SAG

ABSTRACT: To define the sequence of events that lead to the generation of somatic motor neurons (MNs), we took advantage of ESCs, which can be directed to differentiate into spinal neural progenitors (NPs) in vitro (Gouti et al. 2014). This method relies on the exposure of ESCs, cultured as a monolayer, to a brief pulse of Wnt signalling prior to neural induction. Subsequently, removal of Wnt signalling and exposure to retinoic acid (RA) results in the generation of NPs. Exposure of these NPs to Shh signalling agonist SAG induces the expression of genes expressed in the ventral spinal cord and the induction of MNs.

INSTRUMENT(S): Illumina HiSeq 2500, Linux computer, Illumina HiSeq 4000, Fluidigm C1, Linux Beowulf cluster; AMD Opteron Linux Beowulf cluster; AMD Opteron 6168

ORGANISM(S): Mus musculus

SUBMITTER: Jens Kleinjung

PROVIDER: E-MTAB-5466 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Retinoic acid mediated neural and mesoderm specification during vertebrate trunk development

Project description:Neuromesodermal progenitors are located in the caudal lateral epiblast region of embryos and are important for the generation of spinal cord and somite tissue that forms the vertebrate body. In this study we use single cell transcriptomics to define the molecular signature of in vivo and in vitro NMPs and reverse engineer the mechanism that regulates their differentiation towards the neural and mesodermal lineage.

2017-03-22 | E-MTAB-5208 | biostudies-arrayexpress

Selective Death in Spinal Muscular Atrophy: Genome-Wide RNA-Seq Using Purified Patient-Derived Motor Neurons

Project description:Spinal Muscular Atrophy (SMA) is well-known to be caused by mutations in the gene Survival of Motor Neuron 1 (SMN1). Because this gene is ubiquitously expressed, it remains poorly understood why motor neurons (MNs) are one of the most affected cell types. To begin to address this question, we carried out RNA-sequencing studies using fixed, antibody-labeled and purified MNs produced from control and SMA patient-derived induced pluripotent stem cells (iPSCs). We found SMA-specific changes in MNs, including hyper-activation of the endoplasmic reticulum (ER) stress pathway and enhanced apoptosis. Functional studies demonstrated that inhibition of ER stress improves overall MN health and survival in vitro even in MNs with low SMN levels. In SMA mice, we show that systemic delivery of an ER stress inhibitor that crosses the blood-brain-barrier led to preservation of MNs in the spinal cord and prolonged survival of these mice. Therefore, our study implies that selective activation of ER stress underlies MN death in SMA. Moreover, the approach we have taken would be broadly applicable to studying disease-prone human cells in heterogeneous cultures. total RNA collected from ES cell and patient ES cell derived spinal motor neurons

2015-09-01 | E-GEOD-69175 | biostudies-arrayexpress

Gene expression pattern of single mES cells during cell cycle stages

Project description:In this study, we aimed to study the gene expression patterns at single cell level across the different cell cycle stages in mESC. We performed single cell RNA-Seq experiment on mESC that were stained with Hoechst 33342 and Flow cytometry sorted for G1, S and G2M stages of cell cycle. Single cell RNA-Seq was performed using Fluidigm C1 system and libraries were generated using Nextera XT (Illumina) kit.

2014-12-29 | E-MTAB-2805 | biostudies-arrayexpress

Human expression data from iPSCs, motor neurons derived from iPSCs and ESCs, and fetal spinal cords

Project description:We compare transcriptomic profiles of human induced pluripotent stem cells (iPSCs), motor neurons (MNs) in vitro differentiated from iPSCs or human ESCs containing a HB9::GFP reporter for MNs, and human fetal spinal cords. The purpose of this comparison is to assess the extent of molecular similarities between in vitro differentiated MNs and in vivo fetal or adult spinal cord MNs. Data for adult spinal cord MNs are published from other studies: GSE3526, GSE19332, GSE20589, and GSE40438. Human induced pluripotent stem cells, pluripotent stem cell derived motor neurons, and fetal spinal cords for RNA extraction and hybridization on Affymetrix arrays.

2016-06-26 | E-GEOD-75701 | biostudies-arrayexpress

Single cell RNA-sequencing of lineage-negative fraction of stromal cells isolated from inguinal white adipose tissue in mouse

Project description:A subset of adipocytes residing within the inguinal white adipose tissue (ingWAT) of mice exhibit thermogenic activity in response to various external stimuli, including cold exposure. The inducible nature of this thermogenic response, coupled with its robust energy-depleting capacity have prompted investigation into the adipose precursor cells (APCs) from which thermogenic adipocytes derive. To this end, we performed single-cell transcriptomics on cells derived from ingWAT, interscapular brown adipose tissue (iBAT) and epididymal WAT. A subset of single cells collected from ingWAT and epiWAT of mice were chronically (4 days) treated with CL-316,243 (dose at 1 mg kg -1). Tissues of n=28, 10 week-old mice were digested and stromal cells were subsequently purified via differential centrifugation. Single-cell RNA extraction and mRNA amplification were performed on the C1™ Single-Cell Auto Prep Integrated Fluidic Circuit (IFC) following the protocol (PN 100-7168, http://www.fluidigm.com/). Following centrifugation and removal of the medium, cells were resuspended at a concentration of 150–500 cells/μL. This cell suspension was mixed with C1 Cell Suspension Reagent (Fluidigm, Cat # 634833) at the recommended ratio of 3:2 immediately before loading 5 μL of this final mix on the C1 IFC. We obtained, on average, 2.5 million mapped reads per one single cell and successfully reconstructed single-cell expression of ~9,000 genes. Our results revealed a unique cluster of cells that exhibited enriched expression of canonical thermogenic and adipogenic gene markers. Notably, we identified tetraspanin CD81 as a discretely expressed membrane-bound protein conserved specifically within this population. All experiments were performed at our facility at the University of California, San Francisco.

2020-04-24 | E-MTAB-8464 | biostudies-arrayexpress

Single cell mRNA -sequencing reveals cell-to-cell variation in three mouse ES cell culture conditions

Project description:We sequence mRNA from single mESCs from three culture conditions: serum + LIF, 2i + LIF and alternative 2i + LIF. We extensively analysed population and single cell gene expression to identify differences and similarities between conditions. This is a subset of data from ArrayExpress accession E-ERAD-186 (ENA: ERP003293)

2016-01-22 | E-MTAB-2600 | biostudies-arrayexpress

RNA-seq analysis of single cells of the oligodendrocyte lineage from nine distinct regions of the anterior-posterior and dorsal-ventral axis of the mouse juvenile central nervous system

Project description:5069 transcriptomes of single oligodendrocyte cells from spinal cord, substantia nigra-ventral tegmental area, striatum, amygdala, hypothalamic nuclei, zona incerta, hippocampus, and somatosensory cortex of male and female mice between post-natal day 21 and 90. The study aimed at identifying diverse populations of oligodendrocytes, and revealing dynamics of oligodendrocyte maturation. 5069 individual cells were sampled from CNS regions of mice of various strains as detailed in the protocols section

2016-06-10 | E-GEOD-75330 | biostudies-arrayexpress

Single-cell transcriptomics analysis of Lipid A stimulated RAW264.7 cell line

Project description:scRNA-seq analysis of RAW264.7 cells stimulated with 500ng/ml lipidA:Re595 for 3 hours.

2020-07-13 | E-MTAB-9219 | biostudies-arrayexpress

Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms

Project description:We performed single-cell and bulk transcriptome profiling in two different human cell lines. We performed single-cell RNA sequencing in live and fixed cells. Single cell RNA sequencing of live and fixed cells, bulk RNA sequencing in two cell lines.

2015-03-01 | E-GEOD-66053 | biostudies-arrayexpress

A survey of human brain transcriptome diversity at the single cell level

Project description:We used single cell RNA sequencing on 466 cells to capture the cellular complexity of the adult and fetal human brain at a whole transcriptome level. Healthy adult temporal lobe tissue was obtained from epileptic patients during temporal lobectomy for medically refractory seizures. We were able to classify individual cells into all of the major neuronal, glial, and vascular cell types in the brain. Examination of cell types in healthy human brain samples.

2015-05-20 | E-GEOD-67835 | 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