title: Genomic responses to ectopic expression of DHR96 in Drosophila melanogaster

status: Public on Jun 21 2006

city: Edmonton

first: Kirst

last: King-Jones

state: AB

address: 77 University Campus

department: Biological Sciences

institute: University of Alberta

summary:
DHR96 plays a role in regulating xenobiotic responses in Drosophila. Using a gain-of-function approach we test whether DHR96 is sufficient to affect detoxification genes in the absence of a xenobiotic insult.
Keywords: gain-of-function

overall_design: A transgenic line that expresses a full-length DHR96 cDNA under heat-shock control was generated by standard P-element-mediated transformation, using w1118 as a host strain. Control flies are therefore w1118 without any transgene. Larvae were staged at the molt from L2 to L3, and heat-treated after 3 hours for one hour at 37.5 degrees (in vials). Finally, RNA was extracted 4 hours later.

first: Michael

middle: A

last: Horner

first: Geanette

last: Lam

first: Carl

middle: S

last: Thummel


title: Testicular gene expression in SCARKO mice at day 10

status: Public on Oct 04 2005

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary:
To unravel the molecular mechanisms mediating the effects of androgens on spermatogenesis, testicular gene expression was compared in mice with a Sertoli cell-selective androgen receptor knockout (SCARKO) and littermate controls on postnatal d 10. At this age testicular cell composition is still comparable in SCARKOs and controls. Microarray analysis identified 692 genes with significant differences in expression. A more than 2-fold up- or downregulation by androgen action in Sertoli cells was observed for 28 and 6 genes respectively. The biological relevance of the “strongly” upregulated genes was supported by the finding that several of them were previously described to be androgen-regulated or essential for spermatogenesis. Serine protease inhibitors were overrepresented in the same subgroup suggesting a role for androgens in cell junction dynamics and tissue restructuring events during spermatogenesis. A time course experiment (d8-d20), followed by cluster analysis allowed the identification of typical expression patterns of differentially expressed testicular genes during initiation of spermatogenesis. Three genes with a pattern closely resembling that of Pem, a prototypal androgen-regulated gene in Sertoli cells, were selected for confirmation by RT-PCR and further analysis. The data confirm that the SCARKO model allows identification of novel androgen-regulated genes in the testis. This particular series represents  all data from  d 10. The additional expression data from the time course (d8-d20) is represented by series GSE2259 ("Testicular gene expression in SCARKO mice during prepuberty").
Keywords: repeat sample

first: Evi

last: Denolet

first: Karel

last: De Gendt

first: Joke

last: Allemeersch

first: Kristof

last: Engelen

first: Kathleen

last: Marchal

first: Paul

last: Van Hummelen

first: Karen

last: Tan

first: Richard

middle: M

last: Sharpe

first: Philippa

middle: T

last: Saunders

first: Johannes

middle: V

last: Swinnen

first: Guido

last: Verhoeven


title: Testicular gene expression in SCARKO mice during prepuberty

summary:
To unravel the molecular mechanisms mediating the effects of androgens on spermatogenesis, testicular gene expression was compared in mice with a Sertoli cell-selective androgen receptor knockout (SCARKO) and littermate controls on postnatal d 10. At this age testicular cell composition is still comparable in SCARKOs and controls. Microarray analysis identified 692 genes with significant differences in expression. A more than 2-fold up- or downregulation by androgen action in Sertoli cells was observed for 28 and 6 genes respectively. The biological relevance of the “strongly” upregulated genes was supported by the finding that several of them were previously described to be androgen-regulated or essential for spermatogenesis. Serine protease inhibitors were overrepresented in the same subgroup suggesting a role for androgens in cell junction dynamics and tissue restructuring events during spermatogenesis. A time course experiment (d8-d20), followed by cluster analysis allowed the identification of typical expression patterns of differentially expressed testicular genes during initiation of spermatogenesis. Three genes with a pattern closely resembling that of Pem, a prototypal androgen-regulated gene in Sertoli cells, were selected for confirmation by RT-PCR and further analysis. The data confirm that the SCARKO model allows identification of novel androgen-regulated genes in the testis.

This series represents the time course data from d 8, d 10, d 12, d 16 and d 20.
The expression data from the additional SCARKO vs control comparison on d 10
is represented by series GSE2260 ("Testicular gene expression in SCARKO mice at day 10").
Keywords: time-course


title: Genomic responses to Phenobarbital in Drosophila melanogaster

status: Public on Jun 23 2006

country: Canada

summary:
Phenobarbital is a well studied xenobiotic compound. In this study, we describe the genomic responses in fruit flies and examine whether animals mutant for DHR96, an ortholog of xenobiotic nuclear receptors PXR and CAR, plays a role in mediating xenobiotic responses in Drosophila.
Keywords: dose response in mutant vs. wild type

overall_design: Canton S is a commonly used wild type control strain for xenobiotic studies. Wild type or DHR96 mutant flies were starved overnight and then exposed to either sucrose alone or sucrose supplemented with 0.3% Phenobarbital.


title: Sex-specific role of Drosophila HP1 in regulating chromatin structure and gene transcription

status: Public on Aug 05 2005

city: Basel

first: Edward

last: Oakeley

address: Maulbeerstrasse 66

country: Switzerland

institute: FMI

summary:
Drosophila heterochromatin protein 1- HP11 is believed to be involved in active transcription, transcriptional gene silencing, and the formation of heterochromatin2-7. However, little is known about the function of HP1 during development. Using a Gal4-induced RNA interference system, we show that conditional depletion of HP1 in transgenic flies results in preferential lethality in male flies. Cytological analysis of mitotic chromosomes reveals that HP1 depletion causes sex-biased chromosomal defects, including telomere fusions. The global levels of specific histone modifications, particularly the hallmarks of active chromatin, are preferentially increased in males as well. Expression analysis revealed that approximately twice as many genes are specifically regulated by HP1 in males compared to females. Furthermore, HP1-regulated genes showed greater enrichment for HP1 binding in males. Taken together, these results reveal that HP1 modulates chromosomal integrity, histone modifications, and transcription in a sex-specific manner.
Keywords: sex-specific, HP1, gender comparison

overall_design: The extraction of total RNA was performed following a standard protocol (www.erin.utoronto.ca/~w3flyma/protocol.htm). Total RNA was isolated from two independent populations of male and female 3rd-instar larva of HP1-21/act-Gal4 and, as controls, larval progenies from line HP1-21 with the genotype y w; +/+; HP1-21/+, and larva with the genotype y w; + /+; +/act-Gal4. In brief, larvaa frozen in liquid nitrogen were homogenized and then resuspended in Trizol reagent by pipetting. The precipitated RNA was washed, and then dissolved in RNase-free water. Five micrograms of total RNA from each experimental sample were reverse-transcribed using the SuperScript Choice cDNA synthesis kit from Stratagene. One microgram of double-stranded cDNA was in vitro-transcribed using the Affymetrix IVT kit and labeled by the incorporation of biotinylated-UTP. Fifteen micrograms of cRNA were then fragmented and hybridized to Affymetrix DGv2 GeneChips as per the manufacturer’s instructions (Affymetrix, Santa Clara CA, USA).

first: Lu-Ping

last: Liu

first: Jian-Quan

last: Ni

middle: J

first: Fang-Lin

last: Sun


title: Novel cell lines from mouse epiblast share defining features with human embryonic stem cells

status: Public on Jun 27 2007

city: Cleveland

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

country: USA

institute: Case Western Reserve University

summary:
The application of human embryonic stem (ES) cells has an inherent reliance on understanding the starting cell population.  Human ES cells differ from mouse ES cells and the specific embryonic origin of both cell types is unclear.  Previous work suggested that mouse ES cells could only be obtained from the embryo prior to implantation in the uterus.  Here we show that cell lines can be derived from the epiblast, a tissue of the post-implantation embryo that generates the embryo proper.  These cells, which we refer to as EpiSCs (post-implantation epiblast-derived stem cells), express transcription factors known to regulate pluripotency, maintain their genomic integrity, and robustly differentiate into the major somatic cell types as well as primordial germ cells (PGCs).  The post-ES cell lines are distinct from mouse ES cells in their epigenetic state and the signals controlling their differentiation. Furthermore, post-ES and human ES cells share patterns of gene expression and signalling responses that normally function in the epiblast. These results show that epiblast cells can be maintained as stable cell lines and interrogated to understand how pluripotent cells generate distinct fates during early development.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series.


title: Expression data from mammary glands of transgenic mice

status: Public on Dec 20 2006

city: Berlin

first: Andreas

last: Klein

address: Charitéplatz 1

department: Institute of Biochemistry

country: Germany

institute: Charité (CCO)

summary:
The aim of our work was the comparison of human and mouse gene expression data and to identify a conserved breast tumor gene set. The results encourage the usefulness of transgenic mice as a model for human breast cancer formation and therapy.
Keywords: Comparison

overall_design: The aim of our work was to establish a database for breast cancer gene expression data in order to compare human and mouse breast cancer. We identified human and mouse homologues genes and compared the expression profile of 24 human breast tumors with six WAP-SVT/t breast tumors (WAP-SVT/t animals, line 8). Our studies confirmed the heterogeneity in gene expression of human as well as mouse breast cancer cells. However, 63 genes were found to be differentially expressed (upregulated: 40; downregulated: 23 genes) in at least 75% of the breast tumors of both species.


title: CpG island mediated linear and spatial gene partitioning (pA+ RNA-seq profile)

status: Public on Feb 15 2018

city: Austin

first: Jonghwan

last: Kim

state: TX

address: 2506 Speedway NMS 4.246

department: Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology

institute: University of Texas at Austin

type: Expression profiling by high throughput sequencing

summary: In order to test the global effects of CpG island-centered gene regulation on global gene expression profile, pA+ RNA-seq data of diverse tissues and cell lines were gathered and profiled. All available mouse poly-A positive RNA-seq data (3,818 samples) were summarized and downloaded at May, 5th, 2015. Among them, excluding single cell RNA-seq or experiments whose expression verified gene counts are small (less than 5,000 genes with RPKM 0.5 or higher), 1,524 high quality RNA-seq data were used. Raw data were downloaded from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI) database. FASTQ files were extracted with the SRA Toolkit version 2.5.5 and aligned using STAR 2.4.2 onto the mouse and human genome (mm9 and hg19, respectively). Gene expression was calculated as RPKM values using rpkmforgenes.py (Ramsköld et al., 2009).

overall_design: pA+ RNA-seq gene expression analysis in diverse mouse and human samples.

first: Samuel

last: Beck