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SRP106034
Homo sapiens
16 Downloadable Samples
Illumina HiSeq 2500
Description
The differential gene expression of human cardiomyocytes induced by kinase inhibitors sorafenib and sunitinib is measured by a high-throughput mRNA-sequencing approach called 3''-DGE, that is based on a 3'' end-focused reference sequence library and a transcript molecule counting method with unique molecular identifiers (UMI) for correcting PCR bias. Overall design: Cells were treated with sunitinib, sorafenib, or vehicle control for 48 hours, and gene expression levels of all samples were measured by 3''-DGE and conventional random-primed mRNA-sequencing methods using paired-end reading to obtain the genome-wide expression profiles for each sample.
Publication Title
A Comparison of mRNA Sequencing with Random Primed and 3'-Directed Libraries.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Transcriptome analysis of depletion of DYRK1A in HeLa cells
Publication Title
DYRK1A phoshorylates histone H3 to differentially regulate the binding of HP1 isoforms and antagonize HP1-mediated transcriptional repression.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Arabidopsis thaliana
- 41 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Deficiency of the micronutrient zinc is a widespread condition in agricultural soils, generating a negative impact on crop quality and yield. Nevertheless, there is insufficient knowledge on the regulatory and molecular mechanisms underlying the plant response to inadequate zinc nutrition.
Publication Title
Transcriptomic profiling of Arabidopsis gene expression in response to varying micronutrient zinc supply.
Sample Metadata Fields
Age, Specimen part
View Samples- Bos taurus
- 29 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
The aim of this work was to access the early immune response triggered by R. microplus larvae attachment in previously selected resistant and susceptible animals in a bovine F2 population derived from Gyr (Bos indicus) Holstein (Bos taurus) crosses.
Publication Title
Microarray analysis of tick-infested skin in resistant and susceptible cattle confirms the role of inflammatory pathways in immune activation and larval rejection.
Sample Metadata Fields
Specimen part, Time
View Samples- Mus musculus
- 47 Downloadable Samples
- Ion Torrent Proton
Description
We induced mouse embryonic stem cells (ESCs) into B progenitors in in vitro culture. We previously reported that B cells derived from extra-embryonic yolks sac (YS) belong to innate-like B-1 cells, not conventional B-2 cells. Since ES cell differentiation into Blood lineage, it recapitulates YS hematopoiesis, we hypothesized that B cells produced by mouse ESCs belong to B-1 cells as well. We transplanted ESC-derived B-progenitor cells into immunodeficient mice and confirmed that ES-derived B cells differentiate into only B-1 and marginal zone B cells, not B-2 cells in vivo. We preformed gene expression profiles by RNA sequencing comparing ESC-derived, YS-derived, fetal liver derived, and adult bone marrow derived B progenitor cells to see their characteristics. Overall design: We compared gene expression profllings among B-1 progeniotors derived from ES, Yolk sac, and fetal liver, and B-2 progenitors from adult bone marrow. We isolated CD19+B220+ B-progenitor cells obtained from in vitro culture of mouse ES cells, yolk sac, and fetal liver (all B-1 biased) and bone marrow (B-2 biased) and performed RNA sequencing Please note that Flk1 is a marker of mesoderm that differentiate into endothelial cells and blood cells and VEcad (VE-cadherin) is a marker of endothelial cells. It is known that all hematopoietic cells are derived from lateral mesoderm (Flk1+) cells via endothelial phenotype (VE-cad+). Therefore, we differentiated ESCs into Flk1+ mesoderm or VEcad+ endothelial cells and isolated them by sorting (as indicated in the sample source name field), and replated them onto OP9-stromal cells that support B cell development.
Publication Title
Long-Term Engraftment of ESC-Derived B-1 Progenitor Cells Supports HSC-Independent Lymphopoiesis.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA-seq analysis documented mRNA changes in total pancreatic RNA preparations 6 days after Ptf1a inactivation. Overall design: pancreas mRNA profiles of Tamoxifen treated adult control mice [Ptf1a(CreER/+)] and Ptf1a conditional knockout mice [Ptf1a(CreER/fl)] were generated by deep sequencing using an Illumina Hiseq 2500.
Publication Title
Transcriptional Maintenance of Pancreatic Acinar Identity, Differentiation, and Homeostasis by PTF1A.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA-seq analysis of RNA from embryonic day 18.5 pancreas Overall design: pancreas mRNA profiles of E18.5 C57Bl/6 mice were generated by deep sequencing using an Illumina Hiseq 2500.
Publication Title
Transcriptional Maintenance of Pancreatic Acinar Identity, Differentiation, and Homeostasis by PTF1A.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 10 Downloadable Samples
- Illumina HiSeq 2500
Description
Hunger, driven by negative energy balance, elicits the search for and consumption of food. In mammals, this is orchestrated principally through the activity of neurons in the hypothalamus, direct manipulation of which can potently drive food intake. However, the neural circuits outside of the hypothalamus that control feeding are poorly understood. Here, we identify two functionally opponent cell types within the dorsal raphe nucleus (DRN), marked by the vesicular transporters for GABA (Vgat) or glutamate (VGLUT3), that project to many known feeding centers and rapidly control feeding. We find that DRNVgat neurons drive, while DRNVGLUT3 neurons suppress, food intake. Furthermore, through the development and application of cell type-specific molecular profiling technologies, we identify many differentially expressed transmembrane receptors, which may represent unique druggable targets. Local application of agonists for these receptors potently modulates feeding, recapitulating the effects of cell-specific manipulations. Together, these data establish a key role for the DRN in controlling food intake and add an important anatomic site that controls energy balance. Overall design: Paired - Inputs and IPs; Unpaired for Vgat/VGLUT3 comparison
Publication Title
Identification of a Brainstem Circuit Controlling Feeding.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 24 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [AltAnalyz probeset-to-Ensembl mapping (huex10st)
Description
A growing body of evidence points to the essential role of bone marrow (BM) tumor microenvironment in Multiple Myeloma (MM) maintenance and progression. Mesenchymal stem cells (MSC) are one of the most important players in this scenario. Through direct and indirect interactions, these cells support MM cells by promoting increase of proliferation, migration, survival, and drug resistance. Additionally, an increasing number of evidence has been demonstrating that MSC from MM patients (MM-MSC) have several abnormalities when compared with their normal counterpart from normal donors (ND-MSC). Therefore, the aimed of our study was to explore the differences between MM-MSC and ND-MSC through gene expression analysis.
Publication Title
Transcriptome Analysis of Mesenchymal Stem Cells from Multiple Myeloma Patients Reveals Downregulation of Genes Involved in Cell Cycle Progression, Immune Response, and Bone Metabolism.
Sample Metadata Fields
Sex, Age, Specimen part, Disease stage, Subject
View Samples- Mus musculus
- 16 Downloadable Samples
- Illumina HiSeq 4000
Description
Gata2, a zinc finger TF, is essential for the generation and survival of HSCs in the embryo and has been implicated in the pathogenesis of AML, yet the requirement for Gata2 in adult HSCs and LSCs remains unclear. Using a conditional mouse model where Gata2 was deleted specifically in hematopoietic cells, we show that knockout of Gata2 leads to a rapid and complete cell-autonomous loss of adult HSCs. In Meis1a/Hoxa9 driven AML, deletion of Gata2 impedes maintenance and self-renewal of LSCs. We then performed RNA-seq from sorted control and Gata2 KO LSCs (CD45.2+ c-Kit+) after pIpC treatment in transplanted mice. Overall design: Wild Type and Gata2-/- Meis1a/Hoxa9 LSCs were harvested from mice 24 days after pIpC administration
Publication Title
Gata2 as a Crucial Regulator of Stem Cells in Adult Hematopoiesis and Acute Myeloid Leukemia.
Sample Metadata Fields
Cell line, Subject
View Samples