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Total Gene expression analysis of H3f3b null and WT MEFs

ABSTRACT: Total gene expression analysis was performed on constitutive H3f3b KO E12.5 MEFs relative to WT littermates. Intent was to analyze the role of H3f3b in overall gene expression. Constitutive KO mice were obtained by mating H3f3b Fl/Fl mice to Zp3Cre mice. Heterozygous offspring were time mated and embryos were isolated 12.5 days after. MEFs were cultured transduced with a stable pBabe puro vector and total RNA was isolated from H3f3b KO and WT MEFs.

ORGANISM(S): Mus musculus

SUBMITTER: Paul Knoepfler

PROVIDER: E-GEOD-35302 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Total Gene expression analysis of H3f3b null and WT MEFs

Project description:Total gene expression analysis was performed on constitutive H3f3b KO E12.5 MEFs relative to WT littermates. Intent was to analyze the role of H3f3b in overall gene expression.

2013-04-10 | GSE35302 | GEO

Total Gene expression analysis of H3f3b conditional knockout MEFs

Project description:Total gene expression analysis was performed on CRE induced conditional knockout E12.5 MEFs relative to GFP infected control MEFs. Intent was to analyze the role of H3f3b in overall gene expression. For conditional KO, three lines of H3f3b FL/FL E12.5 MEFs (cKO1, cKO2 and pcKO1) were transduced with Cre retroviruses and compared to their respective lines of MEFs transduced solely with GFP vector (as control). Total RNA was isolated for gene analysis.

2013-04-11 | E-GEOD-35301 | biostudies-arrayexpress

Total Gene expression analysis of H3f3b conditional knockout MEFs

2013-04-11 | GSE35301 | GEO

Total Gene expression analysis of H3f3b constitutive knockout testis RNA

Project description:Total gene expression analysis was performed on RNA from testes extracted from two litters of constitutive homozygous and heterozygous H3f3b knockout mice compared to WT littermates. Constitutive knockout mice were obtained by mating H3f3b Fl/Fl mice to Zp3Cre mice. Heterozygous knockout mice were crossed until homozygous knockout mice were obtained. Testes were surgically removed from 8 week old homozygous knockouts, heterozygous knockouts and WT, and RNA was extracted from one testis from each mouse for total gene expression.

2014-07-31 | E-GEOD-35303 | biostudies-arrayexpress

RNA-seq reveals changes in sphingolipid metabolism upon transformation

Project description:We sequenced mRNA from three independent pairs of mock and c-SRC transformed mouse embryonic fibroblasts and examined changes in expression of sphingolipid metabolism genes Three independent cultures of NIH3T3 MEFs were retrovirally transduced with either pBabe-Puro, og pBabe-Puro containing c-srcY527F. After a 7 day of selection in puromycine the three vector and three src transduced pools were propagated for RNA sequencing.

2013-10-17 | E-GEOD-46340 | biostudies-arrayexpress

Endogenous mammalian histone H3.3 exhibits chromatin-related functions during development

Project description:Background. The histone variant H3.3 plays key roles in regulating chromatin states and transcription. However, the role of endogenous H3.3 in mammalian cells and during development has been less thoroughly investigated. To address this gap, we report the production and phenotypic analysis of mice and cells with targeted disruption of the H3.3-encoding gene, H3f3b. Results. H3f3b KO mice exhibit a semi-lethal phenotype traceable at least in part to defective cell division and chromosome segregation. H3f3b KO cells have widespread ectopic CENP-A protein localization suggesting one possible mechanism for defective chromosome segregation. KO cells have abnormal karyotypes and cell cycle profiles as well. The transcriptome and euchromatin-related epigenome were moderately affected by loss of H3f3b in MEFs with ontology most notably pointing to changes in chromatin regulatory and histone coding genes. Reduced numbers of H3f3b KO mice survive to maturity and almost all survivors from both sexes are infertile. Conclusions. Taken together, our studies suggest that endogenous mammalian histone H3.3 has important roles in regulating chromatin and chromosome functions that in turn are important for cell division, genome integrity, and development. Examination of H3K9Ac and H3K4me3 in wild-type and H3.3 null MEFs

2013-04-24 | E-GEOD-34546 | biostudies-arrayexpress

Impact of BHLHE40-AS1 over expression in MCF10A cells

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Endogenous mammalian histone H3.3 exhibits chromatin-related functions during development

2013-04-24 | GSE34546 | GEO

Mutation of GATA3 in Human Breast Tumors

Project description:293T epithelial kidney cell line was infected with retrovirus containing pBabe puro empty plasmid or with pBabe puro plasmid containing either GATA3 wild type or mutation R367-L. Stable colonies were selected, grown, and their mRNAs harvested. mRNA from three independent transfections of 293T cells with the empty plasmid was pooled and used as the reference RNA. Dye flips were performed resulting in four arrays. This series also contains two additional arrays (GSM13007 & GSM13008) not in the publication. Keywords: other

2004-05-24 | GSE841 | GEO

IMR90 hTERT

Project description:Transcription profiling from young and pre-senescent IMR90 cells, transfected either with hTERT (pBabe-puro-hTERT) or vector control (pBabe-puro). Population doubling values are contained in Characteristics[generation] column.

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