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SRP123459
Mus musculus
80 Downloadable Samples
NextSeq 500
Description
Adult neurogenesis in the murine dentate gyrus occurs in a specialized microenvironment that sustains the generation of neurons during life. To fully understand adult neurogenesis, it is essential to determine the neural stem cell (NSC) and progenitor developmental stages, their molecular determinants, and the niche cellular and molecular composition. We report on a single cell RNA sequencing study of the hippocampal niche, performed by isolating all the non-neuronal cell populations. Our analysis provides a comprehensive description of the dentate gyrus cells and allows the identification of exclusive cell type-specific markers. We define the developmental stages and transcriptional dynamics of NSCs and progenitors, and find that while NSCs represent a heterogeneous cellular continuum, progenitors can be grouped in distinct subtypes. We determine the oligodendrocyte lineage and transcriptional dynamics, and describe microglia transcriptional profile and activation state. The combined data constitutes a valuable resource to understand regulatory mechanisms of adult neurogenesis. Overall design: We generated transciptome data from cells unbiasely sorted from the hippocampal neurogenic niche after depleting the neuronal population
Publication Title
A Single-Cell RNA Sequencing Study Reveals Cellular and Molecular Dynamics of the Hippocampal Neurogenic Niche.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 7 Downloadable Samples
- NextSeq 500, Illumina HiSeq 2500
Description
In this study we studied the presence of tumor cells that underwent epithelial-to-mesenchymal transition within polyoma middle T antigen (PyMT) breast tumors. For this we dissociated tumors and isolated Ecad positive tumor cells by FACS sorting. We confirmed that PyMT tumors contain a small set of tumor cells that have undergone EMT in the primary tumor and that E-cadherin can be used as a marker on single cell level for mesenchymal status in this model. Overall design: (i) We isolated primary tumors from mice, dissociated the tumors and FACS-sorted for single Ecad positive tumor cells, after this we performed single cell sequencing of the cells. (ii) We isolated CTCs and solid tumor cells from mice, dissociated the tumors and FACS-sorted for single Ecad positive and negative cells, after this we performed single cell sequencing of the cells.
Publication Title
Plasticity between Epithelial and Mesenchymal States Unlinks EMT from Metastasis-Enhancing Stem Cell Capacity.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 8 Downloadable Samples
- NextSeq 500
Description
The mammary gland is a highly dynamic organ that mainly develops during puberty. Based on morphology and proliferation analysis, mammary stem cells (MaSCs) are thought to be close to or reside in the terminal end buds (TEBs) during pubertal development. However, exclusive stem cell markers are lacking, and therefore the true identity of MaSCs, including their location, multiplicity, dynamics and fate during branching morphogenesis, has yet to be defined. To gain more insights into the molecular identity and heterogeneity of the MaSC pool, we performed single cell transcriptome sequencing of mammary epithelial cells micro-dissected from ducts and TEBs during puberty. These data show that the behaviour of MaSCs cannot be directly linked to a single expression profile. Instead, morphogenesis of the mammary epithelium relies upon a heterogeneous population of MaSCs that functions long-term as a single equipotent pool of stem cells. Overall design: Ducts and terminal end buds were micro-dissected from the 4th and the 5th murine mammary gland at 5 weeks-of-age, dissociated into single cells, and FACS sorted. Single-cell transcriptomics was performed on live cells using an automated version of CEL-seq2 on live, FACS sorted cells. The StemID algorithm was used to identify clusters of cells corresponding to basal and luminal cells types derived from ducts and terminal end buds.
Publication Title
Identity and dynamics of mammary stem cells during branching morphogenesis.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 4 Downloadable Samples
- NextSeq 500
Description
Cell-autonomous circadian oscillations strongly influence tissue physiology and pathophysiology of peripheral organs. Recent in vivo findings in the heart demonstrate that the circadian clock controls oscillatory gene expression programs in the adult myocardium. However, whether in vitro human embryonic stem (ES) cell-derived cardiomyocytes can establish circadian rhythmicity is unknown. Here we report that while undifferentiated human ES cells do not possess a functional clock, oscillatory expression of known core clock genes emerges during directed cardiac differentiation, with robust rhythms in day 30 cardiomyocytes. Our data reveal a stress related oscillatory network of genes that underlies a time-dependent response to doxorubicin, a frequently used anti-cancer drug with cardiotoxic side effects. These results provide a set of oscillatory genes that is relevant to functional cardiac studies and that can be deployed to uncover the potential contribution of the clock to other processes such as cardiac regeneration. Overall design: Human embryonic stem cells (ES cells) were differentiated via a directed differentiation protocol in vitro towards cardiomyocytes for a period of 30 days. Cardiomyocytes were synchronized with dexamethasone and triplicate samples for RNA extraction and sequencing were taken every 4 hours for 48 hours in total. RNA was then extracted using TRIzol, barcoded and amplified following the CEL-Seq protocol.
Publication Title
Circadian networks in human embryonic stem cell-derived cardiomyocytes.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
Lgr5+ stem cells reside at crypt bottoms of the small and large intestine. Small intestinal Paneth cells supply Wnt3, EGF and Notch signals to neighboring Lgr5+ stem cells. While the colon lacks Paneth cells, Deep Crypt Secretory (DCS) cells are intermingled with Lgr5+ stem cells at crypt bottoms. Here, we report Reg4 as a marker of DCS cells. To investigate a niche function, we eliminated DCS cells using the diphtheria-toxin receptor gene knocked into the murine Reg4 locus. Ablation of DCS cells results in loss of stem cells from colonic crypts and disrupts gut homeostasis and colon mini-gut formation. In agreement, sorted Reg4+ DCS cells promote organoid formation of single Lgr5+ colon stem cells. Stem cells are forced to generate DCS cells in vitro by combined Notch inhibition and Wnt activation. We conclude that Reg4+ DCS cells serve as Paneth cell equivalents in the colon crypt niche. Overall design: To define a global gene expression signature of DCS cells, we performed RNA-sequencing (RNA-seq) of sorted Reg4-dsRed+ and Lgr5-GFP+ cells from colonic epithelium. Sorting and RNA-seq library preparation was performed twice, to obtain a biological replicate.
Publication Title
Reg4+ deep crypt secretory cells function as epithelial niche for Lgr5+ stem cells in colon.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 18 Downloadable Samples
- Illumina HiSeq 2500, NextSeq 500
Description
To understand organ (dys)function it is important to have a complete inventory of its cell types and the corresponding markers that unambiguously identify these cell types. This is a challenging task, in particular in human tissues, because unique cell-type markers are typically unavailable, necessitating the analysis of complex cell type mixtures. Transcriptome-wide studies on pancreatic tissue are typically done on pooled islet material. To overcome this challenge we sequenced the transcriptome of thousands of single pancreatic cells from deceased organ donors with and without type 2 diabetes (T2D) allowing in silico purification of the different cell types. We identified the major pancreatic cell types resulting in the identification of many new cell-type specific and T2D-specific markers. Additionally we observed several subpopulations within the canonical pancreatic cell types, which we validated in situ. This resource will be useful for developing a deeper understanding of pancreatic biology and diabetes mellitus. Overall design: Human cadaveric pancreata were used to extract islets of Langerhans, which were kept in culture until single-cell dispersion and FACS sorting. Single-cell transcriptomics was performed on live cells from this mixture using CEL-seq or on cells stained for CD63, CD13, TGFBR3 or CD24 and CD44. The RaceID algorithm was used to identify clusters of cells corresponding to the major pancreatic cell types and to mine for novel cell type-specific genes as well as subpopulations within the known pancreatic cell types.
Publication Title
De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 13 Downloadable Samples
- NextSeq 500, Illumina HiSeq 2500
Description
Paneth cells (PCs) are long-lived secretory cells that reside at the bottoms of small intestinal crypts. Besides serving as niche cells for the neighboring Lgr5-positive stem cells, PCs secrete granules containing a broad spectrum of antimicrobial proteins, including lysozymes and defensins1. Here, we have used single-cell RNA sequencing to explore PC differentiation. We found a maturation gradient from early secretory progenitors to mature PCs, capturing the full maturation path of PCs. Moreover, differential expression of a subset of defensin genes in lysozyme-high PCs, e.g. Defa20, reveals at least two distinct stages of maturation. Overall design: We traced Lgr5+ stem cells from Lgr5-CreERT2 C57Bl6/J mice bred to a Rosa26LSL-YFP reporter mice and sorted YFP+ cells 5 days, 3 weeks and 8 weeks after tamoxifen injection.
Publication Title
De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 58 Downloadable Samples
- NextSeq 500
Description
Data accompaning to van Gurp et al. Development 2019. single-cell sequencing of the developing mouse pancreas followed by Seurat analysis to discover genes important for alpha and beta cell differentiation. Overall design: Single-cells from mouse embryonic pancreas at E12.5, E13.5, E14.5, E15.5 and E18.5 were isolated and enriched for MIP-GFP and sorted into 384-well plates. Afterwards, SORT-seq was performed and single-cell transcriptomics profiles were obtained.
Publication Title
A transcriptomic roadmap to α- and β-cell differentiation in the embryonic pancreas.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 12 Downloadable Samples
Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
We used microarrays to detail the global programme of gene expression during early hESC differentiation to Mesendoderm using FBS.
Publication Title
Lineage-Specific Early Differentiation of Human Embryonic Stem Cells Requires a G2 Cell Cycle Pause.
Sample Metadata Fields
Sex, Cell line, Time
View Samples- Caenorhabditis elegans
- 71 Downloadable Samples
- Illumina HiSeq 2000
Description
The complexity of metazoan organisms requires precise spatiotemporal regulation of gene expression during development. To identify different modes of developmental gene regulation we measured the transcriptome throughout development of the nematode Caenorhabditis elegans by mRNA sequencing with high temporal resolution. We find that approximately 2,000 transcripts undergo expression oscillations synchronized with larval transitions while thousands of genes are expressed in temporal gradients, similar to known timing regulators. By counting transcripts in individual animals, we show that the pulsatile expression of the microRNA (miRNA) lin-4 maintains the temporal gradient of its target lin-14 by dampening its expression oscillations. Our results demonstrate that this insulation is optimal when pulsatile expression of the miRNA and its target is synchronous. We propose that such a miRNA-mediated incoherent feed-forward loop is a potent filter that prevents propagation of potentially deleterious gene expression fluctuations during the development of an organism. Overall design: We analyzed RNA-seq data of wild-type worms at two different temperatures, 20C and 25C, from samples picked every 2hrs and 1.5 hrs, resspectively, spanning all larval stages (L1,L2,L3,L4). At 20C we picked samples for L1-L3 (sample DH2: 0 hrs to 38 hrs) and for L4 (sample DH5: 38 hrs to 48 hrs) from independent populations. At 25C, all samples were picked from the same worm population (sample DH3: 0 hrs to 28.5 hrs). This time course ends at 28.5 hrs since at higher temperature nematode development is accelarated. Finally, we measured mRNA expression at 20C in a lin-4 knockout mutant worm (lin-4(e912)), again spanning all larval stages (sample DH4: 0 hrs to 48 hrs). Each sequencing sample consisted of a mixture of all time points with mRNA from different time points barcoded with Illumina barcodes and was sequenced on one or more lanes (DH2: 3 lanes; DH3: 3 lanes; DH4: 4 lanes; DH5: 1 lane) of an Illumina HiSeq2000.
Publication Title
Dampening of expression oscillations by synchronous regulation of a microRNA and its target.
Sample Metadata Fields
Cell line, Subject
View Samples