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SAGE analysis of cardiac fibroblasts isolated from adult mouse heart

ABSTRACT: Cardiac fibroblasts were isolated from 3-month old C57BL/6 mice. RNA was prepared from quiescent, serum-starved cardiac fibroblasts in passage 15. A total number of 118654 tags was sequenced. After removal of duplicate ditags and linker-derived sequences 110169 tags remained.

ORGANISM(S): Mus musculus

PROVIDER: GSE25757 | GEO | 2010/12/01

SECONDARY ACCESSION(S): PRJNA134049

REPOSITORIES: GEO

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SAGE analysis of cardiac fibroblasts isolated from adult mouse heart

Project description:Cardiac fibroblasts were isolated from 3-month old C57BL/6 mice. RNA was prepared from quiescent, serum-starved cardiac fibroblasts in passage 15. A total number of 118654 tags was sequenced. After removal of duplicate ditags and linker-derived sequences 110169 tags remained. This GEO Series was created by the GEO staff as part of a cleanup effort to ensure that all GEO Samples are included within a Series entry.

2010-12-01 | E-GEOD-25757 | biostudies-arrayexpress

Comprehensive Serial Analysis of Gene Expression of the Cervical Epithelium Transcriptome

Project description:In this study, we sequenced 691,390 SAGE tags from four libraries. Cervical L-SAGE libraries N1, N2, C1, and C2 were sequenced to 165,624, 181,224, 173,534, and 171,008 tags, respectively. Duplicate ditags were eliminated from analysis resulting in 136,276, 139,656, 154,828 and 136,386 useful tags respectively and a total of 24 058 unique tags. 15,438 of the unique tags mapped to annotated UniGene identifiers. We characterized the transcriptome of normal cervical tissue and evaluated the highly expressed genes in terms of tissue specificity, conserved expression among the normal libraries and their altered expression in CIN III lesions. Keywords: Cervical Epithelium, Long SAGE

2008-02-19 | GSE6252 | GEO

Gene expression changes during serum starvation-induced quiescence in human fibroblasts

Project description:We report a comparison of gene expression profiling microarray datasets generated from proliferating and serum-starved quiescent human normal diploid fibroblasts. 4 biological replicates of proliferative and quiescent fibroblasts were subjected to 4 individual dye-swap experiments. Data from these arrays were used in a publication to compare reproducibility between microarrays and RNA-seq; RNA-seq (2 replicates of each proliferative and quiescent fibroblasts) are available through the GEO (accession #: GSE65145). Correlations between both the microarrays and the RNA-seq dataset showed only moderate concordance (r =0.42) in genes exhibiting a ≥5-fold change. Examination of gene expression profiles from prolfierating and quiescent normal human fibroblasts using microarray technology

2015-10-15 | GSE66780 | GEO

MEF wt versus Med23-/- KO after 20% Serum Stimulation

Project description:Affymetrix MOE430A arrays. Mouse embryonic fibroblasts (MEFs) from E11 passaged through crisis. Starved in 0.5% FBS for 16 h then stimulated by 20% serum final concentration for 30 minutes. The purpose was to identify genes affected by the loss of MED23 protein (subunit of the mediator complex). Samples were assayed in duplicate (Set 1 and Set 2) for starved state and serum state cells.

2009-04-14 | GSE15638 | GEO

Lineage Reprogramming of mouse fibroblasts into induced cardiac progenitor cells by defined factors

Project description:Mouse adult cardiac fibroblasts were infected with doxycycline inducible, 11 cardiac factors. Addition of doxycycline resulted in appearance of proliferative cells that had high nuclear-to-cytoplasmic ratio. We called these cells iCPCs. iCPC were stably reporgrammed and could be maintined in proliferative state without doxycycline. Here we compared the transcriptome of iCPC with their parental cells; adult cardiac fibroblasts. We found that iCPCs have upregulated genes involved in cardiovascular development and downregulated fibroblasts specific genes. iCPCs did not expressed endoderm, ectoderm or pluripotency associated genes indicating that they were cardiac mesoderm restricted progenitors. We isolated RNA from low passage iCPCs, high passage iCPCs and cardiac fibroblasts and performed RNASeq analysis

2015-09-16 | E-GEOD-61486 | biostudies-arrayexpress

Comprehensive Serial Analysis of Gene Expression of the Cervical Epithelium Transcriptome

2008-02-18 | E-GEOD-6252 | biostudies-arrayexpress

Grass shrimp SAGE libraries

Project description:Adult male grass shrimp were exposed for 96 hours to LC50 concentrations of either Fipronil, Endosulfan, or Cadmium, as well as a Carrier Control exposure. RNA was extracted from whole-body homogenates using the RNABee kit. Tags were clustered to identify tags diagnostic of the different exposures. Keywords: SAGE, Grass shrimp, ecotoxicogenomics

2006-05-18 | GSE4853 | GEO

RNA sequencing on cardiac fibroblasts harvested at different time points following induction of osteogenic differentiation

Project description:Purpose: To analyze cardiac fibroblasts gene expression at different time following induction of osteogenic differentiation Methods: Freshly isolated cardiac fibroblasts (Passage 0 or passage 1) were plated at a density of 2.5 x 104 cells/cm2 in growth medium. After overnight incubation, osteogenesis was induced using differentiation medium (α-MEM supplemented with 10% FBS, 10 nM dexamethasone (Sigma, D4902), 20 mM β-glycerol phosphate (Sigma, G9422), and 50 μM L-ascorbic acid (Sigma, A4403). Cardiac fibroblasts harvested at Day0 (before differentiation medium treatment), Day7, Day14 and Day21 were used for RNA sequencing. Results: Cardiac fibroblasts harvested at different time points following induction of differentiation revealed clusters of genes whose expression was significantly altered in a temporal specific manner. Genes regulating cell cycle that were highly expressed in undifferentiated cardiac fibroblasts were down-regulated at the onset of differentiation and remained at low expression levels throughout the duration of osteogenic differentiation, consistent with the principle that induction of differentiation is associated with reduced rates of proliferation. In contrast, genes that were minimally expressed in cardiac fibroblasts were induced in a specific temporal manner during the course of osteogenic differentiation and included sets of genes known to regulate inflammation, extracellular matrix proteins and cell metabolism. Conclusions: Cardiac fibroblasts subjected to osteogenic differentiation progressively adopted an osteogenic signature.

2016-11-07 | GSE87836 | GEO

RNA sequencing on EphrinB2 overexpression cardiac fibroblasts and vector cardiac fibroblasts within or without induction of osteogenic differentiation in the 7th day.

Project description:Purpose: To investigate the function of EphrinB2 in the regulation of osteogenic differentiation of cardiac fibroblasts, we established EphrinB2-overexpressing cardiac fibroblasts and corresponding control group by lentivirus.Methods:Adult cardiac fibroblasts were isolated from 6 to 8-week-aged C57BL/6 mice, passage 1 cardiac fibroblasts plated at a density of 2.5 x 104 cells/cm2 were infected with the EphrinB2-overexpressing or vector lentivirus at an MOI of 20 for 12h, after 48 hours’ infection, osteogenesis was induced using differentiation medium (α-MEM supplied with 10% FBS, 10 mM β-glycerophosphate, 100nM dexamethasone and 50 µg/mL L-ascorbic acid). Cardiac fibroblasts harvested at Day7 were used for RNA sequencing.

2022-06-29 | GSE206947 | GEO

The landscape of accessible chromatin in quiescent cardiac fibroblasts and cardiac fibroblasts activated after myocardial infarction

Project description:The landscape of accessible chromatin in quiescent cardiac fibroblasts and cardiac fibroblasts activated after myocardial infarction

| PRJNA772295 | ENA

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