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Transcription profiling of mouse liver from wild type and Foxa2 knock out strains fed on standard diet

ABSTRACT: Transcriptional profiling of changes in global hepatic gene expression in mice lacking Foxa2 in the liver (Foxa2loxP/loxP;Alfp.Cre) on standard rodent diet

ORGANISM(S): Mus musculus

SUBMITTER: Irina Bochkis

PROVIDER: E-MEXP-2106 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcription profiling of mouse liver from wild type and Foxa2 knock out strains fed on a diet supplemented with cholic acid

Project description:Transcriptional profiling of changes in global hepatic gene expression in mice lacking Foxa2 in the liver (Foxa2loxP/loxP;Alfp.Cre) on a diet supplemented with cholic acid, a naturally occurring bile acid

2009-05-08 | E-MEXP-2107 | biostudies-arrayexpress

Chromatin immunopreciptiation of liver from wild type and Foxa2 knock out mice to identify Foxa2 binding sites

Project description:In order to identify the subset of genes directly regulated by Foxa2 in the liver, we performed genome-wide location analysis. Chromatin immunoprecipitation (ChIP) samples from livers of wild type and Foxa2 liver-conditional null mice (Foxa2loxP/loxPAlfp.Cre) were hybridized to a mouse enhancer/promoter microarray with more than 36,000 elements (BCBCPromChip 5). This analysis identified 574 enhancer and promoter regions, corresponding to 484 unique genes, as occupied by Foxa2 in the adult liver.

2008-07-14 | E-MEXP-1675 | biostudies-arrayexpress

Transcription profiling of Aspergillus fumigatus hyphae and conidia after incubation with neutrophils from different donors

Project description:Hyphae and conidia, representing the two developmental stages of the fungus, were examined separately in this study. RNA from hyphae or conidia incubated in plasma in RPMI/HEPES without neutrophils was used as reference, and was co-hybridized with the query samples obtained from the corresponding sets incubated with neutrophils. Each biological replicate was carried out with neutrophils obtained from a different donor, and the RNA samples associated with each neutrophil source was paired separately with a corresponding reference sample prepared at the same time.

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Schladebeck_Whi3_Ploidy

Project description:We analyzed and classified Whi3-regulated and ploidy-regulated genes in haploid and diploid strains of the Sigma1278b genetic background under vegetative growth conditions. For this purpose, we measured transcriptional profiles of two different haploid MATa and one diploid MATa/a yeast strains of the following genotypes: WHI3 strain (SS_YHUM468=YHUM0468), whi3 strain (SS_ySS137=YHUM1920) and whi3-delta/whi3-delta strain (SS_ySS137dipl=YHUM2152). All three strains were grown in duplicate in YNB medium supplemented with tryptophan and uracil at 30 degrees C to an optical density of 1.0 before extraction of total RNA and transcriptional profiling

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MicroRNA profiling of human HeLa cells in hypoxia or normoxia

Project description:Comparison of microRNA expression HeLa cells in hypoxia or normoxia

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Transcription profiling by array of human universal RNA spiked with eight arifical transcripts at different copy numbers

Project description:Examine the dose response characteristics of a set of eight artificial transcripts (IVT) when spiked into a Universal Human RNA background at different copy numbers. The experiment was designed to (i) evaluate the technical reproducibility of array data generated on the Agilent Whole Human 44K array with use of a set of external RNA controls (ii) employ two panels of the same external RNA controls, which differed in copy number between panels, in order to simulate normal and disease states. We employed 8 different pools which were comprised of 8 different external RNA standards in a total human reference RNA background. Each different standard was present at a different copy number within any single pool (see file: E-MEXP-2670.additional.zip). Each control was present at a different concentration in each of the 8 pools. Standard microarray analysis was performed on the data and the differences in abundance between external RNA controls determined in terms of fold change differences.

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2010-01-01 | E-MEXP-2233 | biostudies-arrayexpress

Transcription profiling of human fibrotic liver samples

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2010-04-01 | E-MEXP-2589 | biostudies-arrayexpress

A novel dominant glossy mutation causes suppression of wax biosynthesis pathway and deficiency on cuticular wax in Brassica napus

Project description:The present study reports the genetic and biochemical characterization of a dominant glossy mutant allele (BnaA. GL) in B. napus that results in a glossy phenotype. Results from transmission electron microscopy and scanning electron microscopy revealed the GL mutant exhibits reduced deposition of the cuticle layer, which was confirmed by a cuticular wax analysis. The wax compositional analysis revealed an increase in aldehydes but a severe decrease in alkanes, ketones and secondary alcohols. Genetic mapping narrowed the BnaA. GL gene to the end of A9 chromosome, where a gene homologous to ECERIFERUM1 (CER1) in Arabidopsis locates. Then, we conducted a microarray analysis to find the differentially expressed genes between normal phenotype and glossy plants. Two comparisons were performed: wild type parent VS. the GL parent, and the bulked normal phenotype DH lines VS. the bulked glossy DH lines. The DH lines are generated from F1 plants of two parents, and RNA samples from three DH lines were combined to make a bulked sample for each phenotype. Although no discernible mutation was apparent in the B. napus gene, this cDNA microarray chip assay revealed coordinated down regulation of genes encoding enzymes of the cuticular wax biosynthetic in the glossy mutant with BnCER1 being one of the most severely suppressed genes.

2013-12-07 | E-MEXP-3989 | biostudies-arrayexpress

Transcription profiling of Arabidopsis wild type and srk2dei triple mutant plants in response to abscisic acid, salt and dehydration treatments

Project description:Expression profiles of the wild-type Arabidopsis (Col) and srk2dei triple mutant plants in response to ABA, NaCl, and dehydration treatments.

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