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GSE25198
Macaca mulatta
8 Downloadable Samples
Affymetrix Rhesus Macaque Genome Array (rhesus)
Description
It is often overlooked that human ESCs are generated from in vitro cultured, often surplus/discard, embryos considered unsuitable for transfer in infertility clinics. In vitro culture of preimplantation embryos has been associated with a number of perturbations, including ultrastructure, gene expression, metabolism and post-transfer development. We report here the transcriptional profiles characteristic of ESC lines generated from either in vitro cultured or in vivo derived embryos.
Publication Title
Transcriptional differences between rhesus embryonic stem cells generated from in vitro and in vivo derived embryos.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 46 Downloadable Samples
- Illumina humanRef-8 v2.0 expression beadchip
Description
Numerous studies have shown the potential of spermatozoal RNAs to delineate failures of spermatogenic pathways in infertile samples. However, the RNA contribution of normal fertile samples still needs to be established in relation to transcripts consistently present in human spermatozoa. We report here the spermatozoal transcript profiles characteristic of 24 normally fertile individuals. RNA was extracted from the purified sperm cells of ejaculate and hybridized to Illumina Human-8 BeadChip Microarrays
Publication Title
Identification of human sperm transcripts as candidate markers of male fertility.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Uncontrolled microglial activation may lead to development of inflammation-induced brain damage. Here we uncover a ribosome-based mechanism/check point involved in control of the innate immune response and microglial activation. Using an in vivo model-system for analysis of the dynamic translational state of microglial ribosomes with mRNAs as input and newly synthesized peptides as an output, we find a marked dissociation of microglia mRNA and protein networks following innate immune challenge. Highly up-regulated and ribosome-associated mRNAs were not translated resulting in two distinct microglial molecular signatures, a highly specialized pro-inflammatory mRNA and immunomodulatory/homeostatic protein signature. We find that this is due to specific translational suppression of highly expressed mRNAs through a 3UTR-mediated mechanism involving the RNA binding protein SRSF3. This discovery suggests avenues for therapeutic modulation of innate immune response in resident microglia.
Publication Title
Diverging mRNA and Protein Networks in Activated Microglia Reveal SRSF3 Suppresses Translation of Highly Upregulated Innate Immune Transcripts.
Sample Metadata Fields
Treatment
View Samples- Mus musculus
- 8 Downloadable Samples
Illumina HiSeq 2500
Description
CTSK-mGFP positive cells from Day 6 old mouse femurs were sorted as single cells into 384 well plates pre-loaded with unique barcoded RT-primers. After sorting, cells were snap frozen on dry ice before being submitted to the New York Genome Center (NYGC) for cDNA synthesis and library preparation. The FACS profile for all the sored cells were collected to co-relate with gene expression. Overall design: Mouse femur was obtained from mice within the same litter. Femur samples was subjected to collagenase digestion, and single cell suspension was obtained. The samples were stained for FACS antibodies and single cell sorting was performed into two individual 384 well plates. The experiment has two replicates from two independant animals. The samples were always kept discrete.
Publication Title
Discovery of a periosteal stem cell mediating intramembranous bone formation.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Breast tumorigenesis involves modulation of gene expression.
Publication Title
Nucleotide excision repair deficiency is intrinsic in sporadic stage I breast cancer.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2000
Description
ATP6AP2 is an essential accessory component of the vacuolar H+ ATPase (V-ATPase) and has been associated with intellectual disabilities (ID) and Parkinsonism. ATP6AP2 has been implicated in several signaling pathways, but little is known about its role in the nervous system. To decipher its function in behaviour and cognition, we generated and characterized conditional ATP6AP2 Drosophila and mouse models in the nervous system. In Drosophila, knockdown of ATP6AP2 induced defective phototaxis and vacuolisation of photoreceptor neurons and pigment cells when deleted in eyes and alteration of short- and long-term memory when deleted in the mushroom body. In mouse, conditional Atp6ap2 deletion in glutamatergic neurons (Atp6ap2Camk2aCre/0 mice) caused increased spontaneous locomotor activity and altered memory for fear. Both Drosophila ATP6AP2 knockdown and Atp6ap2Camk2aCre/0 mice presented with presynaptic transmission defect, abnormal number and morphology of synapses, and alteration of axonal transport in fly. In addition, Atp6ap2Camk2aCre/0 mice showed autophagy defect leading to axonal and neuronal degeneration in the cortex and the hippocampus. Surprisingly, myelinisation of axons was affected in our mutant mice. In accordance with the identified phenotypes across species, genome-wide transcriptome profiling of Atp6ap2Camk2aCre/0 mouse hippocampi revealed dysregulated genes involved in myelination, action potential, membrane bound vesicles and adult behaviour. In summary, disruption of ATP6AP2 in mouse and fly leads to cognitive impairment and neurodegeneration, mimicking aspects of the neuropathology associated with ATP6AP2 mutations in humans. Our results identify ATP6AP2 as an essential gene for the nervous system. Overall design: 4 samples, 2 wt and 2 Atp6ap2Camk2aCre/0
Publication Title
Conditional depletion of intellectual disability and Parkinsonism candidate gene ATP6AP2 in fly and mouse induces cognitive impairment and neurodegeneration.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 19 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Integrative analysis of SF-1 transcription factor dosage impact on genome-wide binding and gene expression regulation.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 14 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
SF-1 is a nuclear receptor transcription factor playing a key role in adrenogonadal development and in adrenocortical tumorigenesis when overexpressed. NRSF/REST is a transcriptional repressor that represses expression of neuronal genes in non-neural tissues. Some data suggest that SF-1 and NRSF/REST can functionally interact in adrenocortical cancer cells.
Publication Title
Integrative analysis of SF-1 transcription factor dosage impact on genome-wide binding and gene expression regulation.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
SF-1 is a nuclear receptor transcription factor playing a key role in adrenogonadal development and in adrenocortical tumorigenesis when overexpressed.
Publication Title
Integrative analysis of SF-1 transcription factor dosage impact on genome-wide binding and gene expression regulation.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples- Mus musculus, Homo sapiens
- 30 Downloadable Samples
- Affymetrix Mouse Gene 2.1 ST Array (mogene21st), Affymetrix Mouse Gene 1.1 ST Array (mogene11st), Affymetrix Human Gene 2.1 ST Array (hugene21st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
PML is a ROS sensor activating p53 upon oxidative stress.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Race, Time
View Samples