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Mus musculus
18 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Genome-wide mRNA expression in brains of wild-type and eIF2B-R132H/R132H mutant mice (Geva et al., BRAIN 133 (8), 2010) profiled at postnatal (P) days 1, 18 and 21 to reflect the early proliferative stage prior to white matter establishment (P1) and the peak of oligodendrocye differentiation and myelin synthesis (P18 and P21).
Publication Title
A point mutation in translation initiation factor eIF2B leads to function--and time-specific changes in brain gene expression.
Sample Metadata Fields
Specimen part
View Samples- Drosophila melanogaster
- 10 Downloadable Samples
Illumina Genome Analyzer II
Description
A series of transfections was performed in Drosophila S2 cells to explore: 1) the types of target sites that Drosophila microRNAs recognize, 2) the relative functional efficacy of these sites in mediating repression, and 3) the determinants that allow some sites to have greater potency than others. 3p-seq was also performed to help reannotate and quantify the landscape of 3'' UTRs in Drosophila S2 cells. Overall design: Nine mRNA profiles were generated, with Drosophila S2 cells transfected with one of 6 microRNAs (miR-1, miR-4, miR-92a, miR-124, miR-263a, and miR-997). These samples were compared to 3 biological replicates of a mock transfection condition. 3p-seq data for S2 cells was also generated to help reannotate and quantify 3'' UTR isoforms.
Publication Title
Predicting microRNA targeting efficacy in Drosophila.
Sample Metadata Fields
Specimen part, Subject
View Samples- Danio rerio
- 14 Downloadable Samples
- IlluminaGenomeAnalyzerII, IlluminaHiSeq2000
Description
The post-transcriptional fate of messenger RNAs (mRNAs) is largely dictated by their 3'' untranslated regions (3''UTRs), which are defined by cleavage and polyadenylation (CPA) of pre-mRNAs. We used poly(A)-position profiling by sequencing (3P-Seq) to map poly(A) sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P-Seq reads substantially increased and improved existing 3''UTR annotations, resulting in confidently identified 3''UTRs for more than 78.79% of the annotated protein-coding genes in zebrafish. Most zebrafish genes undergo alternative CPA with more than a thousand genes using different dominant 3''UTRs at different stages. 3''UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest 3''UTRs are highly expressed in the ovary yet absent in the maternally contributed RNAs of the embryo, perhaps because their 3''UTRs are too short to accommodate a uridine-rich motif required for stability of the maternal mRNA. At two hours post-fertilization, thousands of unique poly(A) sites appear at locations lacking a typical polyadenylation signal, which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities, formation, and evolution of zebrafish 3''UTRs provide a resource for studying gene regulation during vertebrate development. Overall design: 3P-Seq was used to map the 3'' ends of protein-coding genes in the zebrafish genome
Publication Title
Extensive alternative polyadenylation during zebrafish development.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 119 Downloadable Samples
- Illumina HiSeq 2500
Description
Messenger RNA is thought to predominantly reside in the cytoplasm, where it is translated and eventually degraded. Although nuclear retention of mRNA has a regulatory potential it is considered extremely rare in mammals. Here to explore the extent of mRNA retention in metabolic tissues we combine deep sequencing of nuclear and cytoplasmic RNA fractions with single molecule transcript imaging in mouse beta cells, liver and gut. We identify a wide range of protein coding genes for which the levels of spliced polyadenylated mRNA are higher in the nucleus than in the cytoplasm. These include genes such as the transcription factor ChREBP, Nlrp6, Glucokinase and Glucagon receptor. We demonstrate that nuclear retention of mRNA can efficiently buffer cytoplasmic transcript levels from noise that emanates from transcriptional bursts. Our study challenges the view that transcripts predominantly reside in the cytoplasm and reveals a role of the nucleus in dampening gene expression noise. Overall design: we have total of 8 samples all are mice. liver nuclear RNA (2 replicates), liver cytoplasmic RNA (2 replicates), MIN6 (cell line) nuclear RNA (2 replicates), MIN6 (cell line) cytoplasmic RNA (2 replicates)
Publication Title
Nuclear Retention of mRNA in Mammalian Tissues.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 2 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
It is now obvious that the majority of cellular transcripts do not code for proteins, and a significant subset of them are long noncoding RNAs (lncRNAs). Many lncRNAs show aberrant expression in cancer, and some of them have been linked to cellular transformation. However, the underlying mechanisms remain poorly understood. Here we characterize the function of the p53-regulated human lncRNA LINC-PINT in cancer. We found that LINC-PINT acts as tumor suppressor lncRNA. Its expression is downregulated in multiple types of cancer and correlates with good prognosis in lung adenocarcinoma. LINC-PINT inhibits the migration capacity and invasive phenotype of cancer cells in vitro and in vivo, and it does so by repressing a proinvasion gene signature in a PRC2-dependent manner. By applying cross-species conservation analysis combined with functional experimental validations we found that the function of LINC-PINT is highly dependent on a short sequence conserved across mammals, sequence that mediates the interaction with PRC2. We propose that LINC-PINT may function as a molecular exchanger that provides PRC2 to active gene promoters for their silencing, mechanisms that could be shared by other PRC2-interacting lncRNAs.
Publication Title
The human lncRNA LINC-PINT inhibits tumor cell invasion through a highly conserved sequence element.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 558 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Establishing reliable biomarkers for assessing and validating clinical diagnosis at early prodromal stages of Parkinsons disease is crucial for developing therapies to slow or halt disease progression. Here, we present the largest study to date using whole blood gene expression profiling from over 500 individuals to identify an 87-gene blood-based signature. Our gene signature effectively differentiates between idiopathic PD patients and controls in both a validation cohort and an independent test cohort, and further highlights mitochondrial metabolism and ubiquitination/proteasomal degradation as potential pathways disrupted in Parkinsons disease.
Publication Title
Analysis of blood-based gene expression in idiopathic Parkinson disease.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Mus musculus
- 10 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The goal of this study is to uncover the changes in the transcriptome of sensory neurons of the liver kinase B1 (LKB1) knockout
Publication Title
Regulation of axonal morphogenesis by the mitochondrial protein Efhd1.
Sample Metadata Fields
Specimen part
View Samples- Gallus gallus
- 1 Downloadable Sample
- Illumina Genome Analyzer IIx
Description
A single replicate of exponentially growing DT40 CL18 chicken B lymphoma cells were harvested and extracted RNA was subjected to Illumina GAIIx paired-end sequencing to determine global gene expression. Overall design: Single replicate RNA-seq expression analysis of DT40 cells.
Publication Title
Third Report on Chicken Genes and Chromosomes 2015.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples
GSE8488- Mus musculus
- 15 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Objectives: To identify similarities and differences in gene expression data in the MEK/ERK and PI3K pathways and to determine how histone modification affects these same pathways.
Publication Title
Regulation of gene expression by PI3K in mouse growth plate chondrocytes.
Sample Metadata Fields
No sample metadata fields
View Samples GSE2154- Mus musculus
- 15 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
Primary micromass cultures derived from 11.5 day old mouse embryo limb buds were cultured for 15 days in differentiating conditions (beta-glycerophosphate and ascorbic acid). Total RNA from differentiating chondrocytes was isolated every three days i.e. days 3,6,9,12 and 15 and hybridized to MOE430A chips. Objective: Gain a view of the temporal gene expression changes occuring during chondrocyte differentiation.
Publication Title
Microarray analyses of gene expression during chondrocyte differentiation identifies novel regulators of hypertrophy.
Sample Metadata Fields
No sample metadata fields
View Samples