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SRP148477
Homo sapiens
973 Downloadable Samples
NextSeq 500
Description
IgE antibodies mediate the symptoms of allergic reactions, yet these antibodies and the cells that produce them remain enigmatic due to their scarcity in humans. To address this, we have isolated single B cells of all isotypes, including rare IgE producing B cells, from the peripheral blood of food allergic individuals. Using single cell RNA sequencing (scRNA-seq) we have characterized the gene expression, splicing, and heavy and light chain antibody sequences of these cells.
Publication Title
High-affinity allergen-specific human antibodies cloned from single IgE B cell transcriptomes.
Sample Metadata Fields
Sex, Age, Specimen part, Disease
View Samples- Saccharomyces cerevisiae
- 15 Downloadable Samples
Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
S288C was transformed with plasmids expressing the GCN5 F221A mutant at varying levels. We sought to examine the global impact on gene expression
Publication Title
Linking yeast Gcn5p catalytic function and gene regulation using a quantitative, graded dominant mutant approach.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
Control and Liver Insulin Receptor KO mice (LIRKO) were sacrificed in the non-fasted state. RNA was prepared from liver samples and subjected to expression microarray analysis
Publication Title
Flavin-containing monooxygenase 3 as a potential player in diabetes-associated atherosclerosis.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 426 Downloadable Samples
- NextSeq 500
Description
With the growing interest in studying primary tissue samples by single cell transcriptome analysis, there is an emerging demand for a preservation strategy that enables sample transportation and storage. In this study, we describe a simple and general strategy that preserves primary tissues at hypothermic temperature. Using FACS and single-cell RNAseq, we demonstrated the effectiveness of this strategy in maintaining cell viability, cell population heterogeneity, and cell transcriptome integrity for primary tissues that underwent up to 3 days of preservation. Overall design: Examine the impact of hypothermic preservation on mouse kidney resident immune cells over up to 4 days at single-cell resolution
Publication Title
High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis.
Sample Metadata Fields
Cell line, Subject, Time
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
WNT5A inhibits metastasis and alters splicing of Cd44 in breast cancer cells.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
A highly metastatic breast cancer cell line, 4T1, was used to generate stable Wnt5a expressing and vector only control cells. Cells were generated using lentivirus infection and selection with blasticidin. Expression of Wnt5a was confirmed using western blot. Cell behaviour was characterized. Wnt5a expressing cells exhibited reduced migration in a transwell assay and reduced metastasis in a tail vein injection assay. Growth was not significantly affected.
Publication Title
WNT5A inhibits metastasis and alters splicing of Cd44 in breast cancer cells.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 20 Downloadable Samples
- Illumina HiSeq 2000
Description
Various mesenchymal cell types have been identified as critical components of the hematopoietic stem/progenitor cell (HSPC) niche. Although several groups have described the generation of mesenchyme from human pluripotent stem cells (hPSC), the capacity of such cells to support hematopoiesis has not been reported. Here we have demonstrated that distinct mesenchymal subpopulations co-emerge from mesoderm during hPSC differentiation. Despite co-expression of common mesenchymal markers (CD73, CD105, CD90, PDGFRß), a subset of cells defined as CD146++CD140alow supported functional HSPC ex vivo while CD146-CD140a+ cells drove differentiation. The CD146++ subset expressed genes associated with the HSPC niche and high levels of the Wnt inhibitors. HSPC support was contact-dependent and was mediated in part through JAG1 expression. Molecular profiling revealed remarkable transcriptional similarity between hPSC-derived CD146++ and primary human CD146++ perivascular cells. The derivation of diverse pools of mesenchymal populations from hPSC opens potential avenues to model their developmental and functional differences and to improve cell-based therapeutics from hPSC. Overall design: Our goal was to analyze and compare transcriptome of human pluripoten stem cell-derived mesenchyme (CD146++ and CD146-) with primary human lipoaspirate tissue-derived pericyte (CD146+) and CD146- mesenchymal populations.
Publication Title
Transcriptionally and Functionally Distinct Mesenchymal Subpopulations Are Generated from Human Pluripotent Stem Cells.
Sample Metadata Fields
Specimen part, Subject
View Samples- Bos taurus
- 12 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Four mature, non-lactating dairy cattle were transitioned from a high forage diet (HF; 0% grain) to a high grain diet (HG; 65% grain) that was fed for three weeks. Rumen papillae biopsies were performed during the HF baseline (week 0) and after the first (week 1) and third week (week 3) of the grain challenge to create a transcript profile for the the short and long-term adaption of the rumen epithelium during ruminal acidosis.
Publication Title
Bovine rumen epithelium undergoes rapid structural adaptations during grain-induced subacute ruminal acidosis.
Sample Metadata Fields
Specimen part, Time
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Studies of adult human hematopoiesis have until now relied on the expression of CD10 to define lymphoid commitment. We report a novel lymphoid-primed population in human bone marrow that is generated from hematopoietic stem cells (HSC) prior to the onset of CD10 expression and B cell commitment, and is identified by high levels of the homing molecule L-selectin (CD62L). CD10-CD62Lhi progenitors have full lymphoid (B/T/NK) potential, and show reduced myeloid and absent erythroid potential. Genome-wide gene expression analysis demonstrates that the CD10-CD62Lhi population represents an intermediate stage of differentiation between CD34+CD38- HSC and CD34+lin-CD10+ progenitors marked by down-regulation of TAL1 and MPL, upregulation of E2A, CD3E and IL2RG expression, and absent B cell commitment or RAG1/2 expression. Immature CD34+CD1a- thymocytes are also CD62Lhi and L-selectin ligands are expressed at the cortico-medullary junction, suggesting a possible role for L-selectin in human thymic homing. These studies identify the earliest stage of lymphoid priming in human bone marrow.
Publication Title
Lymphoid priming in human bone marrow begins before expression of CD10 with upregulation of L-selectin.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- IlluminaHiSeq2000
Description
Although clonal studies of lineage potential have been extensively applied to organ specific stem and progenitor cells, much less is known about the clonal origins of lineages formed from the germ layers in early embryogenesis. We applied lentiviral tagging followed by vector integration site analysis (VISA) with high-throughput sequencing to investigate the ontogeny of the hematopoietic, endothelial and mesenchymal lineages as they emerge from human embryonic mesoderm. In contrast to studies that have used VISA to track differentiation of self-renewing stem cell clones that amplify significantly over time, we focused on a population of progenitor clones with limited self-renewal capability. Our analyses uncovered the critical influence of sampling on the interpretation of lentiviral tag sharing, particularly among complex populations with minimal clonal duplication. By applying a quantitative framework to estimate the degree of undersampling we revealed the existence of tripotent mesodermal progenitors derived from pluripotent stem cells, and the subsequent bifurcation of their differentiation into exclusively bipotent endothelial/hematopoietic or endothelial/mesenchymal progenitors. Overall design: Our goal was to analyze transcriptome changes of mesoderm commitment during human embyronic stem cells differentiation. RNA were extracted and sequenced from two populations, human embryonic stem cells (H1 line) and the human early mesodermal progenitors (hEMP) differentiated from H1.
Publication Title
Transcriptionally and Functionally Distinct Mesenchymal Subpopulations Are Generated from Human Pluripotent Stem Cells.
Sample Metadata Fields
No sample metadata fields
View Samples