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Homo sapiens
6 Downloadable Samples
IlluminaHiSeq2000
Description
There are three major dendritic cell (DC) subsets in both human and mouse, plasmacytoid DCs (pDCs) and two types of conventional DCs (cDCs), cDC1s and cDC2s. cDC2s are important for polarizing CD4+ naive T cells into different subsets including Th1, Th2, Th17, Th22 and regulatory T cells (Tregs). In mice, cDC2s can be further divided into phenotypically and functionally distinct subgroups. However, subsets of human cDC2s have not been reported. In the present study, we showed that human blood CD1c+ conventional DCs (cDC2s) can be further separated into two subpopulations according to their CD5 expression status. Comparative transcriptome analyses showed that the CD5high DCs expressed higher levels of cDC2-specific genes, including IRF4, which is essential for the cDC2 development and its migration to lymph nodes. In contrast, CD5low DCs preferentially expressed monocyte-related genes, including the lineage-specific transcription factor MAFB. Furthermore, compared with CD5low subpopulation, CD5high subpopulation showed stronger migration toward CCL21 and overrepresentation among migratory DCs in lymph nodes. Additionally, the CD5high DCs induced naïve T-cell proliferation more potently than the CD5low DCs. Moreover, CD5high DCs induced higher levels of IL-10-, IL-22- and IL-4-producing T-cell formation, whereas CD5low DCs induced higher levels of IFN-?-producing T-cell formation. Thus, we show that human blood CD1c+ cDC2s encompass two subsets that differ significantly in phenotype, gene expression, and functions. We propose that these two subsets of human cDC2s could potentially play contrasting roles in immunity or tolerance. Overall design: The mRNA profiles of two human blood CD1c+ conventional DCs (cDC2s) subpopulations, in triplicate.
Publication Title
Human Blood CD1c+ Dendritic Cells Encompass CD5high and CD5low Subsets That Differ Significantly in Phenotype, Gene Expression, and Functions.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We sought to identify genes that are regulated by the ovulatory signals in mouse cumulus cells.
Publication Title
Oocyte-dependent activation of MTOR in cumulus cells controls the development and survival of cumulus-oocyte complexes.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 2.1 ST Array (mogene21st)
Description
We sought to identify the potential specific roles of the MTOR signalling in cumulus cells by comparing the transcriptomes of the Control (treated with the DMSO vehicle) and MTOR-specific inhibitor Torin 1(5uM)-treated cumulus-oocyte complexes that were cultured for 16 hours.
Publication Title
Oocyte-dependent activation of MTOR in cumulus cells controls the development and survival of cumulus-oocyte complexes.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Pulmonary hypertension is a frequent consequence of left heart disease and congestive heart failure (CHF) and causes extensive lung vascular remodelling which leads to right ventricular failure. Functional genomics underlying this structural remodelling are unknown but present potential targets for novel therapeutic strategies. We used microarrays to detail the gene expression underlying vascular remodeling in the pathogenesis of pulmonary hypertension and identified distinct classes of up-regulated genes during this process.
Publication Title
Mast cells promote lung vascular remodelling in pulmonary hypertension.
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples
GSE55129- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Purpose:The goals of this study are to understand the mechanisms underlying reduced self-renewal and loss of pluripotency by depletion of Rif1.
Publication Title
Rif1 maintains telomere length homeostasis of ESCs by mediating heterochromatin silencing.
Sample Metadata Fields
Cell line
View Samples- Danio rerio
- 54 Downloadable Samples
- IlluminaHiSeq2500, IlluminaHiSeq2000
Description
Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non-coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation, we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Overall design: Small RNA and mRNA gene expression profiling during 0 and 4 days post amputation.
Publication Title
A Conserved MicroRNA Regulatory Circuit Is Differentially Controlled during Limb/Appendage Regeneration.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
To identify downstream targets of Jak/Stat3 pathways without being distracted by differentiation signalings from MEK/ERK pathway, we exploited a engineered B6 cells, which stably stably expressing a chimeric receptor (GRgp-Y118F). The chimeric receptor can induce the phosphorylation of Stat3 by GCSF without activating the MEK/ERK pathway. To mimic the effect of GCSF, the chimeric B6 cells were also treated with LIF plus a selective MEK chemical inhibitor, PD0325901, to induce LIF/Jak/Stat3 but MEK/ERK pathways.
Publication Title
Gbx2, a LIF/Stat3 target, promotes reprogramming to and retention of the pluripotent ground state.
Sample Metadata Fields
Cell line
View Samples- Danio rerio
- 6 Downloadable Samples
- IlluminaHiSeq2000
Description
Purpose: We report the application of NGS for profiling the impacts of PCP exposure on the transcriptome of zebrafish embryos. Methods: mRNA profiles of 10 hpf/24 hpf PCP-treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: At 24 hpf, 6087 transcripts were affected after 200 µg/l exposure, in which 3593 were up-regulated and 2494 were down-regulated, and 1783 transcripts were affected after 5 µg/l exposure, in which 1031 were up-regulated and 752 were down-regulated. At 10 hpf, 2970 transcripts were affected after 200 µg/l exposure, in which 1526 were up-regulated and 1444 were down-regulated, and 1366 transcripts were affected after 5 µg/l exposure, in which 521 were up-regulated and 845 were down-regulated. Conclusions: This study provides a framework for the application of high-throughput RNA sequencing towards characterization of the impacts of PCP on whole zebrafish larval transcriptome. Overall design: Examination of zebrafish embronic transcriptomes with 2 concentrations and 2 durations of PCP treatments.
Publication Title
The developmental effects of pentachlorophenol on zebrafish embryos during segmentation: A systematic view.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 57 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
The recovery of liver mass is mainly mediated by proliferation and enlargement of hepatocytes after partial hepatectomy. Studying the gene expression profiles of hepatocytes after partial hepatectomy will be helpful in exploring the mechanism of liver regeneration.
Publication Title
<i>In silico</i> analysis of expression data during the early priming stage of liver regeneration after partial hepatectomy in rat.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Danio rerio
- 48 Downloadable Samples
- Illumina HiSeq 2500
Description
The adult zebrafish is capable of regenerating heart muscle, resolving collagen tissue and fully restoring heart function throughout its life. The goal of this study was to investigate how the highly upregulated, epicardium-enriched microRNA let-7i functions in wound closure and cardiomyocyte proliferation. We found that depletion of let-7 in adult zebrafish using locked-nucleic acid (LNA) antisense oligonucleotides results in defective heart regeneration. We assayed gene expression at 7 days post ventricular resection in LNA-scrambled and LNA-anti-let-7 treated adult zebrafish to determine the role of let-7 during heart regeneration. Overall design: mRNA gene expression profiling at 7 days post ventricular resection in LNA-scrambled and LNA-anti-let-7 treated zebrafish.
Publication Title
Modulation of TNFα Activity by the microRNA Let-7 Coordinates Zebrafish Heart Regeneration.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples