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Homo sapiens
12 Downloadable Samples
IlluminaHiSeq2500
Description
To determine the global effects of ASCT2 inhibition, we used next generation sequencing to determine mRNA expression changes in PC-3 cells treated with BenSer or GPNA for 48 h. Overall design: Examination of two different ASCT2 inhibitors BenSer and GPNA in prostate cancer cell line PC-3.
Publication Title
Targeting ASCT2-mediated glutamine uptake blocks prostate cancer growth and tumour development.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 24 Downloadable Samples
- Illumina HiSeq 4000
Description
In this study, isotretinoin (INN)-induced alternations in transcriptome during caidiomyocyte differentiation derived from human hESCs and hiPSCs were investigated. H1-hESC and C15-hiPSC were differentiated to caidiomyocytes under exposure to sublethal level of INN, and cells were collected at day 0 (undifferentiated cellsl) day 2 (mesoderm) and day 6 (cardiac progenitors) for genome-wide transcriptomic profiling by RNA-seq. Overall design: H1-hESC and C15-hiPSC were grown in 12-well plates with Essential 8 medium (Thermo Fisher Scientific), and the cardiomyocyte differentiation was initiated using a monolayer differentiation method with PSC Cardiomyocyte Differentiation kit (Thermo Fisher Scientific) under exposure to 25nM of isotretinoin (INN). At day 0, 2 and 6 during the differentiation period (before the medium-change on that day), and cells were collected using Accutase (Thermo Fisher Scientific), and then store in -80C till RNA isolation. For each cell line and each time-point, cells from two independent differentiation wells were used as two biological replicates. RNA-seq libriries were constructed using ScriptSeqâ„¢ v2 RNA-Seq Library Preparation kit (Epicentre Biotechnologies), and then sequenced by a HiSeq 4000 sequencer (Illumina) with 2 X 101 cycles. RNA-seq fastq data were aligned with Tophat (version 2.0.9) to GRCh39/hg19 Homo sapiens reference genome from the UCSC Genome Browser. The human gene symbols and their raw counts were calculated using HTSeq (version 0.6.1p1) package in Python with GRCh39/hg19 Homo sapiens gtf file. Differential gene-expression analysis was performed using edgeR package in R, and the normalization was performed using a trimmed mean of M-values (TMM) method.
Publication Title
Disruption of mesoderm formation during cardiac differentiation due to developmental exposure to 13-cis-retinoic acid.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The reduced folate carrier (RFC1) is an integral membrane protein and facilitative anion exchanger that mediates delivery of 5-methyltetrahydrofolate into mammalian cells. Adequate maternal-fetal transport of folate is necessary for normal embryogenesis. Targeted inactivation of the murine RFC1 gene results in post-implantation embryo lethality, but daily folic acid supplementation of pregnant dams prolongs survival of homozygous embryos until mid-gestation. At E10.5 RFC1-/- embryos are developmentally delayed relative to wildtype littermates, have multiple malformations, including neural tube defects, and die due to failure of chorioallantoic fusion. The mesoderm is sparse and disorganized, and there is a marked absence of erythrocytes in yolk sac blood islands. Affymetrix microarray analysis and quantitative RT-PCR validation of the relative gene expression profiles in E9.5 RFC1-/- vs. RFC1+/+ embryos indicates a dramatic downregulation of multiple genes involved in erythropoiesis, and upregulation of several genes that form the cubilin-megalin multiligand endocytic receptor complex. Megalin protein expression disappears from the visceral yolk sac of RFC1-/- embryos, and cubilin protein is widely misexpressed. Inactivation of RFC1 impacts the expression of several ligands and interacting proteins in the cubilin-amnionless-megalin complex that are involved in the maternal-fetal transport of folate, vitamin B12, and other nutrients, lipids and morphogens required for normal embryogenesis.
Publication Title
Microarray analysis of E9.5 reduced folate carrier (RFC1; Slc19a1) knockout embryos reveals altered expression of genes in the cubilin-megalin multiligand endocytic receptor complex.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 10 Downloadable Samples
- Illumina HiSeq 2500, Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP).
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 10 Downloadable Samples
Illumina HiSeq 2500, Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
RNA binding proteins (RBPs) play essential roles in cellular physiology by interacting with target RNAs. As defects in protein-RNA recognition lead to human disease, UV-crosslinking and immunoprecipitation (CLIP) of ribonuclear complexes followed by deep sequencing (-seq) is critical in constructing protein-RNA maps to expand our understanding of RBP function. However, current CLIP protocols are technically demanding and involve low complexity libraries that yield squandered sequencing of PCR duplicates and high experimental failure rates. To enable truly large-scale implementation of CLIP-seq, we have developed an enhanced CLIP methodology (eCLIP) that features a decrease of ~10 cycles of requisite amplification with a concomitant >60% decrease in discarded PCR duplicate reads, while maintaining the ability to identify RNA binding with single-nucleotide resolution. By simplifying the generation of paired IgG and size-matched input controls, eCLIP also dramatically improves specificity in discovery of authentic binding sites. To demonstrate that eCLIP enables large-scale and robust profiling of RBPs, 102 eCLIP experiments in biological duplicate for a diverse collection of 74 RBPs in HepG2 and K562 cells were completed (available at https://www.encodeproject.org). We establish that eCLIP is comparable in amplification and sample requirements to ChIP-seq, and enables integrative analysis of diverse RBPs to reveal factor-specific profiles, common artifacts for CLIP experiments and RNA-centric perspectives of RBP activity.
Publication Title
Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP).
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 285 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
This series represents 180 lymph-node negative relapse free patients and 106 lymph-node negate patients that developed a distant metastasis.
Publication Title
Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
Activated T cells inhibit neurogenesis in adult animal brain and cultured human fetal neural stem cells (NSC). However, the role of inhibition of neurogenesis in human neuroinflammatory diseases is still uncertain because of the difficulty in obtaining adult NSC from patients. Recent developments in cell reprogramming suggest that NSC may be derived directly from adult fibroblasts. We generated NSC from adult human peripheral CD34+ cells by transfecting the cells with Sendai virus constructs containing Sox-2, Oct3/4, C-MyC and Klf-4. The derived NSC could be differentiated to astroglia and action potential firing neurons. Co-culturing NSC with activated autologous T cells or treatment with recombinant granzyme B caused inhibition of neurogenesis as indicated by decreased NSC proliferation and neuronal differentiation. Thus, we have established a unique autologous in vitro model to study the pathophysiology of neuroinflammatory diseases that has potential for usage in personalized medicine.
Publication Title
Derivation of neural stem cells from human adult peripheral CD34+ cells for an autologous model of neuroinflammation.
Sample Metadata Fields
Specimen part
View Samples
GSE62993- Arabidopsis thaliana
- 9 Downloadable Samples
- Arabidopsis Gene 1.0 ST Array (aragene10st)
Description
We have identified the causal genes, which is MYB36, of ionome mutants.
Publication Title
The MYB36 transcription factor orchestrates Casparian strip formation.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 30 Downloadable Samples
- Illumina HiSeq 3000
Description
Metabolic engagement is intrinsic to immune cell function. Prostaglandin E2 (PGE2) has been shown to modulate macrophage activation, yet how PGE2 might affect metabolism is unclear. Here we show that PGE2 causes mitochondrial membrane potential (??m) to dissipate in interleukin-4 activated macrophages (M(IL-4)). Effects on ??m are a consequence of PGE2-initiated transcriptional regulation of genes in the malate-aspartate shuttle (MAS), particularly GOT1. Reduced ??m causes alterations in the expression of 126 voltage regulated genes (VRGs) including Resistin like molecule-a (RELMa), a key marker of M(IL-4), and genes that regulate cell cycle. The transcription factor ETS variant 1 (ETV1) plays a role in the regulation of 38% of the VRGs. These results reveal ETV1 as a ??m-sensitive transcription factor, and ??m as a mediator of mitochondrial-directed nuclear gene expression. Overall design: RNA-seq was performed on bone marrow derived macrophages (triplicate) exposed to IL-4 alone or in combination with PGE2 or Valinomycin plus no stimulation controls. In addition, RNA-seq was performed on bone marrow derived macrophages stimulated in the same way as before, however the transcription factor ETV1 was knocked down.
Publication Title
Mitochondrial Membrane Potential Regulates Nuclear Gene Expression in Macrophages Exposed to Prostaglandin E2.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus, Homo sapiens
- 63 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20), Illumina HiSeq 2000
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.
Sample Metadata Fields
Age, Specimen part, Disease, Cell line, Treatment
View Samples