GEO DataSets

Analysis of retinas of C57BL/6J animals deficient for H6 family homeobox 1 (HMX1). Loss of Hmx1 function in humans results in an oculoauricular defect leading to eye and auricular developmental abnormalities as well as early retinal degeneration. Results provide insight into role of Hmx1 in retina.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 2 genotype/variation sets

Platform:

GPL6246

Series:

GSE47002

8 Samples

Download data: CEL

(Submitter supplied) Hmx1 is a transcription factor expressed in the developing eye and ear and in some other parts of the nervous system. Dumbo mice are carrying the Hmx1 p.Q64X loss-of-function mutation (Munroe et al., 2009. BMC Developmental Biology). Transcriptomic analyses of this mouse model allows to decipher biological pathways under the control of Hmx1. In our study, we used it to better understand the role of Hmx1 in the retina and to identify several of its target genes.

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS4810

Platform:

GPL6246

8 Samples

Download data: CEL, TXT

(Submitter supplied) RNA Polymerase-II active regions were mapped comparing mouse neural retina tissue at age P25 and P2 to find novel gene activation predictions during maturation of photoreceptors. Over 800 predictions of increased activation were novel compared to previous mRNA expression array studies.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5811

3 Samples

Download data: BED, CEL

(Submitter supplied) CRX is a key transcript factor for photoreceptor development and homeostasis. We have characterized the CRX-dependent cis-regulatory network by ChIP-chip analysis of 2 month old BL/6 mouse retinas using Affymetrix Mouse Promoter 1.0 arrays

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5811

1 Sample

Download data: BED, CEL, TXT

(Submitter supplied) In chicks, the avian homologue of the early growth response protein-1 (ZENK) has been shown to be increased in a special cell type of the retina, the glucagonergic amacrine cells, under conditions that lead to a reduction in eye growth (myopic defocus, recovery of myopia) and decreased under conditions that enhance ocular growth (hyperopic defocus, form-deprivation). The investigation of Egr-1 knock-out mice showed that homozygous knock-out mice with no functional Egr-1 protein developed relative axial myopia at the age of 42 and 56 days, compared to heterozygous- and wildtype Egr-1 knock-out mice. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS3607

Platform:

GPL1261

16 Samples

Download data: CEL

Analysis of retinas of Egr-1 deficient animals at post-natal days 30 and 42. 42 day-old Egr-1 knockout animals have longer eyes and a more myopic refractive error compared to wild-types. Results provide insight into the molecular mechanisms regulating axial eye growth.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 age, 2 genotype/variation sets

Platform:

GPL1261

Series:

GSE16974

16 Samples

Download data: CEL

(Submitter supplied) For each sample a matched total was prepared in parallel. For each biological replicate the cells were crosslinked on different days. Amplicons were prepared from each sample and hybridized on mouse 1.5 kb promoter arrays from Nimblegen. Keywords: ChIP-chip

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3793

14 Samples

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(Submitter supplied) Suz12 samples are biological replicates from F9 cells crosslinked on different days. EZH2 and H3me3K27 samples are from the same batch of crosslinked cells as Suz12 replicate 2. For each sample matched total was prepared in parallel. Amplicons were made and hybridized on custom genomic tiling arrays. Keywords: ChIP-chip

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3794

4 Samples

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(Submitter supplied) For each sample a matched total was produced in parallel. Amplicons were made from each and hybridized on human 5.0 kb promoter arrays from Nimblegen. Keywords: ChIP-chip

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3791

3 Samples

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(Submitter supplied) These samples are biological replicates from Ntera cells that were crosslinked on different days. For each sample a matched total was produced in a parallel. Amplicons were made from each and hybridized on human 1.5 kb promoter arrays from Nimblegen. Keywords: ChIP-chip

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3787

4 Samples

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(Submitter supplied) All samples are from the same batch of crosslinked Ntera cells with a matched total produced in parallel. Amplicons were made from each and hybridized on ENCODE region tiling arrays. Two color arrays were used; ChIP was red, Total was green. Keywords: ChIP-chip

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3792

4 Samples

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(Submitter supplied) This is an integrative genome-wide approach to identify downstream networks controlled by Pax6 during mouse lens and forebrain development. Differential gene expression was analyzed in Pax6 mouse heterozygous and wildtype newborn mouse lenses, with subsequent comparison of this data with Pax6 forebrain expression data (Holm et al., 2007). Keywords: Differential gene expression

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL8321

6 Samples

Download data: CEL

(Submitter supplied) HOXA5 inducible cell line Hs578T was established and cultured as described previously (MCB 2004. 24:924-935). 2×106 cells were seeded onto a 10-cm cell culture dish at 24h before induction. Two batches of RNA from HOXA5-inducible cells (0 h, 6 h and 9 h) were purified for repeating the microarray hybridization experiments once using Affymatrix Chips.Total RNA was extracted using TRIzol reagent (Gibco BRL, Life Technologies, Grand Island, NY) and purified using the RNeasy Mini Kit (Qiagen, Valencia, CA). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

6 Samples

Download data

(Submitter supplied) We present a microarray experiment with the same tet-inducible system but with multiple time points within 24 hr to capture early responses to Oct4 suppression. These data were analyzed together with published genome-wide ChIP data. We found that most tentative target genes (TTG) of Oct4 in ES cells were activated by Oct4 and only a few genes were suppressed. The same method was then applied to find target genes of Sox2 and Nanog based mostly on previously published data. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL4358 GPL2549 GPL2552

40 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by array

Platforms:

GPL4128 GPL10333 GPL4129

28 Samples

Download data: TXT

(Submitter supplied) Genetic investigations of X-linked intellectual disabilities have implicated the ARX (Aristaless-related homeobox) gene in a wide spectrum of disorders extending from phenotypes characterised by severe neuronal migration defects such as lissencephaly, to mild or moderate forms of mental retardation without apparent brain abnormalities but with associated features of dystonia and epilepsy. Analysis of Arx spatio-temporal localisation profile in mouse revealed expression in telencephalic structures, mainly restricted to populations of GABAergic neurons at all stages of development. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10333

16 Samples

Download data: TXT

(Submitter supplied) Genetic investigations of X-linked intellectual disabilities have implicated the ARX (Aristaless-related homeobox) gene in a wide spectrum of disorders extending from phenotypes characterised by severe neuronal migration defects such as lissencephaly, to mild or moderate forms of mental retardation without apparent brain abnormalities but with associated features of dystonia and epilepsy. Analysis of Arx spatio-temporal localisation profile in mouse revealed expression in telencephalic structures, mainly restricted to populations of GABAergic neurons at all stages of development. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL4128 GPL4129

12 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Methylation profiling by array; Expression profiling by array

Platforms:

GPL14550 GPL14835

36 Samples

Download data: TXT

(Submitter supplied) To screen candidate methylation markers for early detection of breast cancer, we performed methylated-CpG island recovery assay combined with CpG island array on 61982 CpG sites across 4162 genes in 10 breast tumor tissues and 10 non-tumor breast tissues. We detected 70 significantly hypermethylated genes in breast tumor tissues, including many novel hypermethylated genes such as ITGA4, NFIX, OTX2 and FGF12. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

16 Samples

Download data: TXT

(Submitter supplied) To screen candidate methylation markers for early detection of breast cancer, we performed methylated-CpG island recovery assay combined with CpG island array on 61982 CpG sites across 4162 genes in 10 breast tumor tissues and 10 non-tumor breast tissues. We detected 70 significantly hypermethylated genes in breast tumor tissues, including many novel hypermethylated genes such as ITGA4, NFIX, OTX2 and FGF12. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL14835

20 Samples

Download data: TXT