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ERP001552
Danio rerio
22 Downloadable Samples
IlluminaHiSeq2000
Description
Zebrafish were raised at temperatures of either 27C or 32C as embryos. After hatching, fish were raised to adulthood at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and after 30 days acclimation 16C.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 8 Downloadable Samples
- Illumina HiSeq 2000
Description
Based on the pkl dP mutant phenotype, it is predicted that PKL plays a key role in regulating GA-responsive genes that are important for vegetative growth and phase transitions. To test this hypothesis, global transcriptome analysis was performed by RNA-Seq using shoots of 13d-old ga1-13 and ga1-13 pkl that were mock-treated or 10 µM GA3-treated for 24 h.
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus, Homo sapiens
- 24 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Lineage-Specific Differentiation Is Influenced by State of Human Pluripotency.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 11 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
While disease recurrence remains the outstanding clinical challenge in acute myeloid leukemia (AML), the basis of relapse remains poorly characterized and thereby preventing effective therapeutic targeting. We performed gene expression analysis of human AML patient samples in addition to in vitro and in vivo assays of leukemic cell survival and self-renewal using xenograft modeling. These molecular and functional analyses afforded the identification of unique target genes that support recurrence. Preclinical modeling using these novel targets provided proof-of-principle for combination therapies towards more effective and durable suppression of AML regrowth.
Publication Title
Identification of Chemotherapy-Induced Leukemic-Regenerating Cells Reveals a Transient Vulnerability of Human AML Recurrence.
Sample Metadata Fields
Specimen part
View Samples- Gallus gallus
- 23 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
Cell transformation by the Src tyrosine kinase is characterized by extensive changes in gene expression. To describe these changes, investigators have relied extensively on the study of immortalized rodent cell lines or heterogeneous tumor samples that limit the identification of differentially expressed genes or may not represent the full spectrum of biological processes regulated during transformation. In this study, we took advantage of transformation-deficient and temperature sensitive mutants of the Rous sarcoma virus to characterize the patterns of gene expression in two types of primary cells, namely chicken embryo fibroblasts (CEF) and chicken neuro-retinal (CNR) cells.
Publication Title
Cellular processes of v-Src transformation revealed by gene profiling of primary cells--implications for human cancer.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 22 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Human induced pluripotent stem cells (hiPSCs) provide an invaluable source for regenerative medicine; but are limited by proficient lineage specific differentiation. Here we reveal that hiPSCs derived from dermal skin fibroblasts (Fib) vs. human cord blood (CB) cells exhibit equivalent and indistinguishable pluripotent properties, but harbor important propensities for neural and hematopoietic lineage differentiation, independent of reprogramming factors used. Genes associated with germ layer specification were identical in both Fib or CB derived iPSCs; whereas patterns of lineage specific marks emerge upon differentiation induction of hiPSCs that were correlated to the cell type of origin used to create hiPSCs. Functionally, CB-iPSCs predominantly differentiate into hematopoietic cells and even adopt definitive hematopoiesis as evidenced by adult -globin positive red blood cell development whereas Fib-iPSCs possess enhanced neural capacity. These clear differentiation propensities come at the expense of other lineages and cannot be overcome with additional external stimuli for alternative cell fates. Moreover, these differences in developmental potential are encoded within cultures of CB vs. Fib derived hiPSCs that can be used to predict differentiation propensity.
Publication Title
Somatic transcriptome priming gates lineage-specific differentiation potential of human-induced pluripotent stem cell states.
Sample Metadata Fields
Specimen part
View Samples- Gallus gallus
- 20 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
To investigate the role of AP-1 in Src-mediated transformation, we undertook a gene profiling study to characterize the transcriptomes of v-Src-transformed CEF expressing either the c-Jun dominant-negative mutant TAM67 or JunD shRNA.
Publication Title
JunD/AP-1 Antagonizes the Induction of DAPK1 To Promote the Survival of v-Src-Transformed Cells.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 18 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Human pluripotent stem cells (hPSCs) have been reported in nave and primed states. However, the ability of human PSCs to generate mature cell types is the only imperative property for translational utility. Here, we reveal that the nave state enhances self-renewal capacity while restricting lineage differentiation in vitro to neural default fate. Gene expression analyses indicate expression of multiple lineage associated transcripts in nave hPSCs and thus failed to predict biased functional differentiation. Nave hPSCs can be converted to primed allowing recovery of multilineage differentiation over long serial passage or immediately through suppression of OCT4 but not NANOG. To this end, we identified chemical inhibitors of OCT4 expression that acutely restore nave hPSC differentiation. Our study identifies unique cell fate features and critical restrictions in human pluripotent states, and provides an approach to overcome these barriers that harness both efficient nave hPSC growth whilst maintaining in vitro differentiation capacities essential for hPSC applications.
Publication Title
Lineage-Specific Differentiation Is Influenced by State of Human Pluripotency.
Sample Metadata Fields
Specimen part
View Samples- Xenopus laevis x xenopus borealis, Xenopus borealis, Xenopus muelleri, Xenopus laevis
- 4 Downloadable Samples
- Affymetrix Xenopus laevis Genome Array (xenopuslaevis)
Description
Gene expression was examined in testis and brain tissue between two species (Xenopus laevis and Xenopus borealis) and their hybrid.
Publication Title
Single-species microarrays and comparative transcriptomics.
Sample Metadata Fields
Age
View Samples- Homo sapiens
- 3 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Human pluripotent stem cells (hPSC) generate hematopoietic progenitor cells (HPC), but fail to engraft xenograft models, which is a hallmark feature of adult/somatic hematopoietic stem cells (HSC) from human donors. Progress to derive hPSC-derived HSCs has relied on cell autonomous approaches that force expression of transcription factors (TF), however the role of bone marrow (BM) niche remains poorly understood. Here, we quantified a failure of hPSC-HPCs to survive even in the first 24 h upon transplantation into the BM. Across several hPSC-HPC differentiation methodologies, we identified the lack of CXCR4 expression and network function. Ectopic CXCR4 conferred CXCL12-dependent signaling of hPSC-HPCs in biochemical assays and increased migration/chemotaxis and progenitor capacity, as well as survival and proliferation following transplantation in vivo. In addition, hPSC-HPCs forced to express CXCR4 demonstrated a transcriptional shift toward somatic HPCs, but this approach failed to produce long-term HSC engraftment. Our results reveal that independent of differentiation methods, networks involving CXCR4 should be targeted to generate HSCs with in vivo function from hPSCs.
Publication Title
CXCL12/CXCR4 Signaling Enhances Human PSC-Derived Hematopoietic Progenitor Function and Overcomes Early In Vivo Transplantation Failure.
Sample Metadata Fields
Specimen part
View Samples