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GSE62067
Homo sapiens
9 Downloadable Samples
Illumina HumanHT-12 V4.0 expression beadchip
Description
The polyadenosine RNA binding proteins (Pabs) represent one class of RNA binding proteins that play critical roles in gene expression. This class includes the well-studied nuclear and cytoplasmic Pabs, PABPN1 and PABPC1, respectively, as well as the newly characterized nuclear Pab, zinc finger CCCH-type containing #14, or ZC3H14. ZC3H14 was recently linked to a form of intellectual disability, suggesting a critical role for ZC3H14 in neurons; however, the post-transcriptional function of ZC3H14 is unknown. In this study, we performed a microarray analysis of cells depleted of ZC3H14 or PABPN1 in MCF-7 breast cancer cells. These results revealed that PABPN1 significantly affected ~17% of expressed transcripts as compared to ZC3H14, which affected ~1% of expressed transcripts, suggesting that ZC3H14 has specific mRNA targets. The differentially expressed mRNAs identified in this analysis not only provide information about the classes and types of transcripts that are regulated by these proteins, but also represent a set of transcripts that could be directly bound by ZC3H14 and/or PABPN1.
Publication Title
The Polyadenosine RNA-binding Protein, Zinc Finger Cys3His Protein 14 (ZC3H14), Regulates the Pre-mRNA Processing of a Key ATP Synthase Subunit mRNA.
Alternate Accession IDs
Sample Metadata Fields
Cell line
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This study analyzes transcriptome profiles in pre-germinated seeds and hypoxia-treated seedlings of Arabidopsis thaliana wild type (Col-0) and homozygous mutants (prt6-1 and ate1 ate2). This dataset includes CEL files, RMA signal values and MAS5 P/M/A calls. For pre-germinated seeds, seeds imbibed for 24 h were used for total RNA extraction. For hypoxia treatment, 7-d-old seedlings were incubated in a hypoxia chamber for 2 h and the entire seedling was subjected to RNA extraction. Quantitative profiling of cellular mRNAs was accomplished with the Affymetrix ATH1 platform. Changes in the transcriptome during early seed germination stage and in response to hypoxia in seedlings were evaluated. The data led to identification of mRNAs with abundance regulated by PRT6 and ATE1 / ATE2, which are essential components for the N-end rule pathway of targeted proteolysis (NERP). A combination of genetic, biochemical and molecular analyses reveal that NERP coordinates the stability of key ethylene responsive factor (ERF) family transcription factors, which regulate expression of core hypoxia response genes and tolerance to low oxygen stress. This indicates that the NERP functions as a homeostatic sensor of low oxygen in plants.
Publication Title
Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants.
Alternate Accession IDs
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Microarray experiments were performed using FAC-sorted young photoreceptors to analyze their transcriptome in comparison to remaining retinal cells at same developmental stage and retinal progenitors.
Publication Title
Increased integration of transplanted CD73-positive photoreceptor precursors into adult mouse retina.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
Illumina Genome Analyzer IIx
Description
Purpose: The goal of this study was to compare and contrast the next generation sequencing data to data obtained from a whole brain microarray study Overall design: Examination of the effects of Glyceollin alone, 17ß Estradiol alone or in combination on gene expression in the adult female mouse brain
Publication Title
Next generation sequencing analysis of soy glyceollins and 17-β estradiol: Effects on transcript abundance in the female mouse brain.
Alternate Accession IDs
Sample Metadata Fields
Sex, Cell line, Subject
View Samples- Mus musculus
- 99 Downloadable Samples
- Illumina HiSeq 2500
Description
Our study demonstrated that e-cigarettes, both with and without nicotine, induced sex-dependent gene expression change. This RNA-seq study examined the expression profiles of brain frontal cortex samples from mice exposed to classic tobacco flavored bluâ„¢ e-cigarettes during gestation and lactation. Overall design: Brains were extracted and sectioned from ~1-month-old male and female offspring the week following exposure, RNA was isolated and purified from frontal cotrex tissues, and gene expression profiles were analyzed by RNA Sequencing.
Publication Title
Microglia Activation and Gene Expression Alteration of Neurotrophins in the Hippocampus Following Early-Life Exposure to E-Cigarette Aerosols in a Murine Model.
Alternate Accession IDs
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
The BM-derived CD45+/Sca1+ cells are haematopoietic stem/progenitor cells that have the ability to circulate and migrate and engraft to the muscle tissue, and therefore they are of particular interest. Notably, these cells retain their haematopoietic potential, as revealed both by in vitro and in vivo assays; but they also acquire myogenic potential, as shown by their ability to participate in muscle regeneration. Whether, this latter remarkable ability is the result of the reprogramming of the BM-CD45+/Sca1+ cells and the activation of a myogenic molecular program within these cells, remains controversial. This study aims to clarify this aspect of the process, investigating the role of the muscle microenviroment and key myogenic transcription factors.
Publication Title
Bone marrow-derived hematopoietic cells undergo myogenic differentiation following a Pax-7 independent pathway.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Schizosaccharomyces pombe
- 8 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Opi10 is the S. pombe homolog of human Hikeshi, which imports Hsp70s into the nucei during the heat shock.
Publication Title
The Schizosaccharomyces pombe Hikeshi/Opi10 protein has similar biochemical functions to its human homolog but acts in different physiological contexts.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 17 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Temporal changes of the expression levels of the complete human transcriptome during the first 24 hours following infection of IFN-pre-treated macrophages. This approach has allowed us to identify genes involved in the IFN signaling that have an impact on HIV-1 infection of macrophages
Publication Title
TRAF6 and IRF7 control HIV replication in macrophages.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Time
View Samples- Mus musculus
- 35 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
The aim of this study was to investigate the molecular mechanisms implicated in this mouse model of nemaline myopathy, and to further compare the molecular disease response in different skeletal muscles. For this purpose, snap frozen skeletla muscle specimens from wild type and transgenic for alpha tropomyosin slow mice were studied. Five different muscle types were used (diaphragm, plantaris, extensor digitorum longus, tibialis anterior, gastrocnemus). Mice were sacrificed between 7 and 10 months. RNA pools from 3-5 animals were created and each pool was hybridized to a U74Av2 Affymetrix GeneChip. Datasets from 36 GeneChips were included in this study.
Publication Title
Skeletal muscle repair in a mouse model of nemaline myopathy.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 21 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The effects of 7.5 micromolar parthenolide (PTL) were assessed on primary CD34+ acute myelogenous leukemia specimens obtained from 12 patients.
Publication Title
Discovery of agents that eradicate leukemia stem cells using an in silico screen of public gene expression data.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
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