Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Neural stem and progenitor cells shorten S-phase upon commitment to neuron production

ABSTRACT: The dorsal telencephalon from E14.5 Tis21–GFP heterozygous mice embryos was subjected to microarray analysis. To identify genes whose expression were changed in Tis21–GFP positive S phase cells compared to Tis21–GFP negative S phase cells, Tis21–GFP positive or negative S phase cells labeled with a vital dye were separated by FACS corresponding to the GFP expression and DNA contents of the cells. 30 telencephalic hemispheres from 15 embryos of the Tis21–GFP heterozygous mice at E14.5 were dissected to collect approximately 200,000 S phase cells either from Tis21–GFP positive or negative for one replicate. Four independent experiments were performed from 3 different pregnant mice at least for each experiment set. Finally three best experiment sets were used for data analyses.

ORGANISM(S): Mus musculus

SUBMITTER: Yoko Arai

PROVIDER: E-GEOD-23585 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Expression data from mouse limb tendon cells during development.

Project description:We have undertaken a screen of mouse limb tendon cells in order to identify molecular pathways involved in tendon development. Mouse limb tendon cells were isolated based on Scleraxis (Scx) expression at different stages of development: E11.5, E12.5 and E14.5 Microarray comparisons were carried out between tendon progenitor and differentiated stages. Forelimbs from E11.5, E12.5 and E14.5 Scx-GFP embryos were collected and dissociated with trypsin to obtain cell suspensions. Scx-positive tendon cells were isolated by FACS. RNA was extracted and Fragmented biotin-labelled cRNA samples were hybridized on Affymetrix Gene Chip Mouse Genome 430 2.0 arrays.

2014-01-18 | E-GEOD-54207 | biostudies-arrayexpress

Expression profiling of Noto-GFP+ notochord progenitor cells sorted from E8.5 mouse embryos

Project description:Using a combination of cell sorting and microarray analysis, we identified almost 200 genes as having a high level of expression in the notochord. After whole mount in situ hybridization screening, we confirmed approximately one third of these as having a novel notochord expression pattern. Keywords: cell type comparison - embryonic Noto-GFP+ notochord progenitors versus surrounding GFP- comparator cells 3 biological replicates - each replicate includes an experiment cell population (Noto-GFP positive cell sort) and a comparator population (GFP negative cell sort)

2011-09-30 | E-GEOD-14211 | biostudies-arrayexpress

Neural stem and progenitor cells shorten S-phase upon commitment to neuron production

Project description:The dorsal telencephalon from E14.5 Tis21–GFP heterozygous mice embryos was subjected to microarray analysis. To identify genes whose expression were changed in Tis21–GFP positive S phase cells compared to Tis21–GFP negative S phase cells, Tis21–GFP positive or negative S phase cells labeled with a vital dye were separated by FACS corresponding to the GFP expression and DNA contents of the cells.

2010-11-30 | GSE23585 | GEO

Analysis of differential gene expression during functional beta-cell maturation in the mouse

Project description:Global gene expression is tested in FACS-sorted beta-cells from PDX1-GFP transgenic mice at different ages (E18.5, P1, P10 and adult) Total RNA obtained from FACS-sorted beta-cells from PDX1-GFP transgenic mice at different ages (E18.5, P1, P10 and adult)

2012-02-18 | E-GEOD-35906 | biostudies-arrayexpress

Screening for micropeptides in HUVEC without tryptic digestion, part 1

Project description:Long non-coding RNAs (lncRNA) are transcribed but not translated ribonucleic acids with various functions. We analyzed a so far unreported lncRNA n342419, which we named MANTIS. A search for micropeptides after overexpression of MANTIS in Human Umbilical Vein Endothelial Cells (HUVEC) with subsequent LC-MS/MS without trypsination showed that none of the micropeptides found had any similarity to potential MANTIS ORFs, whereas the positive control yielded micropeptides encoded from GFP plasmid.

2017-03-27 | PXD005951 | Pride

The niche for extramedullar hematopoiesis in the spleen

Project description:Adult hematopoietic stem cells (HSCs) reside primarily in bone marrow. However, hematopoietic stresses such as myelofibrosis, anemia, pregnancy, infection or myeloablation can mobilize HSCs to the spleen and induce extramedullary hematopoiesis (EMH). While the bone marrow HSC niche has been studied intensively, the EMH niche has received little attention. Here, we systematically assessed the physiological sources of the key niche factors, SCF and CXCL12, in the mouse spleen after EMH induction by cyclophosphamide plus granulocyte colony-stimulating factor, blood loss, or pregnancy. In each case, Scf was expressed by endothelial cells and Tcf21+ stromal cells, primarily around sinusoids in red pulp, while Cxcl12 was expressed by a subset of Tcf21+ stromal cells. EMH induction markedly expanded the Scf-expressing endothelial cells and stromal cells by inducing proliferation. Most splenic HSCs were adjacent to Tcf21+ stromal cells in red pulp. Conditional deletion of Scf from spleen endothelial cells or Scf or Cxcl12 from Tcf21+ stromal cells severely reduced spleen EMH and reduced blood cell counts without affecting bone marrow hematopoiesis. Endothelial cells and Tcf21+ stromal cells thus create the splenic EMH niche, which is necessary for the physiological response to diverse hematopoietic stresses. Unfractionated spleen cells (2 replicates) and FACS-sorted VE-cadherein negative Scf-GFP positive cells (3 replicates)

2015-08-01 | E-GEOD-71288 | biostudies-arrayexpress

An RNA-interacting protein network regulates pluripotency in mammalian primordial germ cells (in vitro, in vivo)

Project description:Primordial germ cells (PGCs) are the embryonic precursors to egg and sperm. When removed from the embryonic gonad, PGCs can give rise to embryonic germ cell lines (EGs), pluripotent stem cells that display most of the characteristics of embryonic stem cells (ESCs) including the ability to form teratomas and to contribute to chimera formation. In mice, EG cells can be derived between E8.5 up to E12.5 of embryonic development, at which point the PGCs undergo sexual differentiation and in the male transition into unipotent gonocytes. Dazl, a germ cell-specific RNA-binding protein, is specifically expressed in developing PGCs and is required for proper germ cell development. Dazl knockout mice are infertile, but the molecular mechanisms underlying this phenotype are still unknown. Here we demonstrate that Dazl localizes in granular structures in mammalian PGCs but not in ESCs. We demonstrate Dazl plays a central role in a large mRNA/protein interactive network that includes members of Fragile-X family RNA-binding proteins. We demonstrate that Dazl and Fxr1 play a central role in these granules and directly regulate the translation of specific core pluripotency factors, including Sox2 and Suz12. Global gene expression changes during in vitro germ cell differentiation from murine ES cells and comparison to in vivo germ cells. In vitro primordial germ cells differentiated from Stella-GFP ES cells and Dazl-GFP ES cells. The GFP-positive cells were isolated by FACS analysis. Dazl-GFP+ cells were isolated from transgenic E13.5 embryonic gonads and P7-P11 juvenile mouse testes. The global gene expression profiles were analyzed by Agilent Mouse Whole Genome 4X44K one-color microarrays. Two replicates per condition.

2013-12-31 | E-GEOD-39546 | biostudies-arrayexpress

Chronological expression data from mouse skeletal muscle stem cells

Project description:Satellite cells are the primary source of stem cells for skeletal muscle growth and regeneration. Since adult stem cell maintenance involves a fine balance between intrinsic and extrinsic mechanisms, we performed genome-wide chronological expression profiling to identify the transcriptomic changes involved in acquisition of muscle stem cell characteristics. Muscle samples were isolated from the trunk during development, postnatally and in adult and aged Pax3GFP/+ mice. After digestion, GFP cells were purified via FACS and process for RNA extraction and hybridization on Affymetrix microarrays (Affymetrix Mouse Genome 430 2.0 Arrays). The different ages selected for sample isolation were E11.5-E12.5-E13.5-E14.5-E15.5-E17.5-P1-P12-1MO-2MO-18MO (E, Embryonic days; P, Postnatal days; MO, age in months), covering embryonic and fetal progenitors and proliferant, quiescent satellite cells. The eleven stages were done in triplicate for E11.5-E12.5-E14.5-E15.5-1MO-2MO-18MO, twice for E13.5, 4 times for P1-P12 and 5 times for E17.5, so 36 samples included in the microarray.

2016-06-15 | E-GEOD-63860 | biostudies-arrayexpress

Transcription profiling of mouse TfRc deficient and wild type renalcells in chimeric embryonic kidneys derived from embryos created by blastocyst injection

Project description:We investigated the ability of transferrin receptor1 (TfRc) knockout cells to populate different domains of the developing kidney by using a chimeric approach. The TfRc cells developed into all segments of the developing nephron, but there was a relative exclusion from the ureteric bud and a positive bias towards the stromal compartment. Here we conducted a microarray analysis of differential gene expression between TfRc deficient and wild type (wt) cells in chimeric embryonic kidneys derived from embryos created by blastocyst injection of wt blastocysts with TfRc-/- green fluorescent protein-expressing (GFP+) embryonic stem cells. Experiment Overall Design: Following blastocyst injection of 3-5 TfRc-/- GFP+ embryonic stem cells in wt blstocysts, we harvested the chimeric kidney at day E15.5 and separated the TfRc-/- GFP+ cell population from wt GFP- cell population by using fluorescence activated cell sorting. Biotinlyated cRNA was prepared from the isolated cells and hybridized to Mouse Genome 430 2.0 Arrays (Affymetrix) according to standard protocols.

2008-10-18 | E-GEOD-7396 | biostudies-arrayexpress

Ascl1, Nurr1 and Lmx1 convert mouse and human fibroblasts into functional dopaminergic neurons without passing through an intermediate precursor state

Project description:Lineage-specific transcription factors, which drive cellular identity during embryogenesis, have been shown to convert cell fate when express ectopically in heterologous cells. Herein, we screened the key molecular factors governing the dopaminergic neuronal specification during brain development for their ability to generate similar neurons directly from mouse and human fibroblasts. Remarkably, we found a minimal set of three factors Mash1, Nurr1 and Lmx1a/b able to elicit such cellular reprogramming. Molecular and transcriptome studies showed reprogrammed DA neurons to faithfully recapitulate gene expression of their brain homolog cells while lacking expression of other catecholaminergic neuronal types. Induced neurons showed spontaneous electrical activity organized in regular spikes consistent with the pacemaker activity featured by brain DA neurons. The three factors were able to elicit DA neuronal conversion in human fibroblasts from prenatal or adult fibroblasts of healthy donors and a Parkinson’s disease patient. Generation of DA induced neurons from somatic cells might have significant implications in studies of neural development, disease in vitro modeling and cell replacement therapies. We infected mouse embryonic fibroblasts (MEFs) isolated from TH-GFP knock-in mice embryos at E14.5, with lentiviruses expressing the three dopaminergic transcription factors Ascl1, Lmx1a and Nurr1. TH-GFP MEFs infected (Ind) by a pool of the three previously mentioned dopaminergic lentiviruses were shifted in a neuronal medium for 12 days and sorted for GFP-positive cells. Thus we extracted mRNA from Ind-GFP-positive cells and compared them to not infetced (NI) cells by means of RNA-microarray analysis.

2011-07-04 | E-GEOD-27174 | 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