Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Signalling molecules in MEFs/FL

ABSTRACT: In silico analysis identified signalling molecules related to Wnt (Wnt1, 2, 5a, 5b, 6, 11, 14, Wisp1, 2, sFRP1 and 2, Dkks 2 and 3) and BMP (BMP1, 4, 5) pathways. Many of these tags matched multiple transcripts in GenBank, while other potential molecules could not be detected because the transcripts either lacked an anchoring enzyme site or the site was immediately adjacent to the polyA+ sequence. Keywords: SAGE To identify potential signalling molecules (secreted or cell-cell interacting) implicated in the formation of INPs, we constructed a SAGE library from MEFs

ORGANISM(S): Mus musculus

SUBMITTER: Kenneth Boheler

PROVIDER: E-GEOD-5402 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Signals from embryonic fibroblasts induce adult intestinal epithelial cells to form nestin-positive cells with proliferation and multilineage differentiation capacity in vitro.

Wiese Cornelia C Rolletschek Alexandra A Kania Gabriela G Navarrete-Santos Anne A Anisimov Sergey V SV Steinfarz Barbara B Tarasov Kirill V KV Brugh Sheryl A SA Zahanich Ihor I Rüschenschmidt Christiane C Beck Heinz H Blyszczuk Przemyslaw P Czyz Jaroslaw J Heubach Jürgen F JF Ravens Ursula U Horstmann Olaf O St-Onge Luc L Braun Thomas T Brüstle Oliver O Boheler Kenneth R KR Wobus Anna M AM

Stem cells (Dayton, Ohio) 20060601 9

The intestinal epithelium has one of the greatest regenerative capacities in the body; however, neither stem nor progenitor cells have been successfully cultivated from the intestine. In this study, we applied an "artificial niche" of mouse embryonic fibroblasts to derive multipotent cells from the intestinal epithelium. Cocultivation of adult mouse and human intestinal epithelium with fibroblast feeder cells led to the generation of a novel type of nestin-positive cells (intestinal epithelium-d ...[more]

PMID: 16741226

Similar Datasets

Signalling molecules in MEFs/FL

Project description:In silico analysis identified signalling molecules related to Wnt (Wnt1, 2, 5a, 5b, 6, 11, 14, Wisp1, 2, sFRP1 and 2, Dkks 2 and 3) and BMP (BMP1, 4, 5) pathways. Many of these tags matched multiple transcripts in GenBank, while other potential molecules could not be detected because the transcripts either lacked an anchoring enzyme site or the site was immediately adjacent to the polyA+ sequence. Keywords: SAGE

2006-07-27 | GSE5402 | GEO

Expression Data from ST2 cells treated with Wnt1

Project description:Wnt1 has major anabolic functions in bone metabolism. We investigated the effect of recombinant murine Wnt1/Sfrp1 complex on the mesenchymal cell line ST2. We used microarray analysis to detail the global gene expression of ST2 cells in response to 6 hour of treatment with 100 ng recombinant Wnt1/Sfrp1 complex.

2022-08-17 | GSE211391 | GEO

Zebrafish ovarian follicle transcriptome

Project description:SAGE analysis of fully grown ovarian follicles has been carried out to supply a resource for identification of important molecules involved in vertebrate oogenesis and in early stages of embryonic development. Keywords: SAGE About 250 full-grown ovarian follicles were obtained after gentle squeezing the abdomen of five mature zebrafish females.

2006-03-17 | E-GEOD-3679 | biostudies-arrayexpress

Wisp inhibits chondrogenic differentiation in heterotopic ossification

Project description:Heterotopic ossification (HO) is the formation of extra-skeletal bone in muscle and soft tissues. Better characterization of the signaling pathways predisposing to HO is critical to identifying therapies directed against this common and potentially debilitating condition. WISP-1 (WNT1-inducible-signaling pathway protein 1) is a CCN family member and is expressed in skeletal cells during bone development or repair. Here, we sought to comprehensively explore the significance of WISP-1 across mouse and human HO. Among CCN family members, local Wisp1 expression was most highly upregulated within experimental trauma-associated HO by RNA sequencing, and increased Wisp1 corresponded to gene markers of osteochondral differentiation. WISP1 immunolocalization demonstrated conserved expression in osteochondral cells across mouse and human HO, including an FOP-like model, post-traumatic model, and human examples of non-genetic HO. Transgenic Wisp1 global knockout demonstrated an increase in cartilage and bone in a trauma-induced HO model. Microarray and in vitro culture of Wisp1 null cells suggested that WISP1 functions as a negative regulator of chondrogenic differentiation, and that Wisp1 deletion results in unrestrained endochondral HO formation. siRNA mediated WISP1 knockdown in human progenitor cells confirmed this finding. Overall, these findings suggest that endogenous WISP1 has pathophysiologic relevance in trauma-induced HO and functions as a negative regulator of ectopic chondrogenesis.

2020-06-08 | GSE127956 | GEO

Transcriptional profiling of inductive prostatic mesenchyme

Project description:Background: The mesenchymal compartment plays a key role in organogenesis and cells within the mesenchyme/stroma are a source of potent molecules that control epithelia during development and tumourigenesis. We have used Serial Analysis of Gene Expression (SAGE) to profile a key subset of prostatic mesenchyme that regulates prostate development and is enriched for growth-regulatory molecules. Results: SAGE libraries were made of prostatic inductive mesenchyme (VMP) and the complete prostatic rudiment (including inductive mesenchyme, epithelium and smooth muscle; VSU). By comparing these two SAGE libraries we generated a list of 219 transcripts that were enriched or specific to inductive mesenchyme and which may act as mesenchymal regulators of organogenesis and tumourigenesis. Conclusions: The use of a precisely defined subset of cells, and a back-comparison approach, allowed us to identify rare mRNAs that might be overlooked using other approaches. Keywords: SAGE, gene profiling Two SAGE libraries were prepared and compared to each other. The VMP forms a subset of the VSU.

2007-12-20 | E-GEOD-7899 | biostudies-arrayexpress

Detecting novel low-abundant transcripts in Drosophila

Project description:Increasing evidence suggests that low-abundant transcripts may play fundamental roles in biological processes. In an attempt to estimate the prevalence of low-abundant transcripts in eukaryotic genomes, we performed a transcriptome analysis in Drosophila using the SAGE technique. We collected 244,313 SAGE tags from transcripts expressed in Drosophila embryonic, larval, pupae, adult, and testicular tissue. From these SAGE tags, we identified 40,823 unique SAGE tags. Our analysis showed that 55% of the 40,823 unique SAGE tags are novel without matches in currently known Drosophila transcripts, and most of the novel SAGE tags have low copy numbers. Further analysis indicated that these novel SAGE tags represent novel low-abundant transcripts expressed from loci outside of currently annotated exons including the intergenic and intronic regions, and antisense of the currently annotated exons in the Drosophila genome. Our study reveals the presence of a significant number of novel low-abundant transcripts in Drosophila, and highlights the need to isolate these novel low-abundant transcripts for further biological studies. Keywords: other

2005-06-03 | E-GEOD-2347 | biostudies-arrayexpress

The pattern of gene expression in human CD34(+) stem/progenitor cells

Project description:We have analyzed the pattern of gene expression in human primary CD34(+) stem/progenitor cells. We identified 42,399 unique serial analysis of gene expression (SAGE) tags among 106,021 SAGE tags collected from 2.5 x 10(6) CD34(+) cells purified from bone marrow. Of these unique SAGE tags, 21,546 matched known expressed sequences, including 3,687 known genes, and 20,854 were novel without a match. The SAGE tags that matched known sequences tended to be at higher levels, whereas the novel SAGE tags tended to be at lower levels. By using the generation of longer sequences from SAGE tags for gene identification (GLGI) method, we identified the correct gene for 385 of 440 high-copy SAGE tags that matched multiple genes and we generated 198 novel 3' expressed sequence tags from 138 high-copy novel SAGE tags. We observed that many different SAGE tags were derived from the same genes, reflecting the high heterogeneity of the 3' untranslated region in the expressed genes. We compared the quantitative relationship for genes known to be important in hematopoiesis. The qualitative identification and quantitative measure for each known gene, expressed sequence tag, and novel SAGE tag provide a base for studying normal gene expression in hematopoietic stem/progenitor cells and for studying abnormal gene expression in hematopoietic diseases. Keywords: other

2005-02-28 | E-GEOD-2346 | biostudies-arrayexpress

expression array

Project description:SFRP1 functions as an important inhibitor of the Wnt pathway and is a known tumor suppressor gene, which is epigenetically silenced in a variety of tumors. Nevertheless, too little is known about signaling pathways modulated by forced SFRP1 re-expression in dependency of the molecular breast cancer subtypes. In this study, we performed a systematic expression analysis of stably transfected human breast cancer cells to determine those molecules and biochemical pathways affected after forced SFRP1 re-expression.

2014-12-01 | E-MTAB-2209 | biostudies-arrayexpress

Global transcriptome analysis of mouse uterus during embryo implantation by SAGE

Project description:The aim of this study was to examine differential gene expression profile in mouse uterus on day 5 of pregnancy between implantation sites and inter-implantation sites. There are 104,520 tags sequenced and acquired, 51,306 for non-implantation site, and 53,214 for implantation site. Keywords: Implantation, Uterus, Differential gene expression, Implantation sites and inter-implantation sites were isolated from the mouse uteri on day 5 of pregnancy from at least 20 mice. Implantation sites were identified by tail-vein injection of 0.1 ml of 1% Chicago blue 5 min before sample collection. SAGE analysis was used to examine differential gene expression in mouse uterus during embryo implantation.

2005-07-13 | E-GEOD-2892 | biostudies-arrayexpress

eye-SAGE

Project description:Human retinal and RPE SAGE libraries. Profile of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium determined through serial analysis of gene expression (SAGE). Keywords: other

2001-10-03 | E-GEOD-10 | 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