Filters
Technology
Platform
SRP093880
Mus musculus
118 Downloadable Samples
NextSeq 500
Description
In multicellular organisms, dedicated regulatory circuits control cell-type diversity and response. The crosstalk and redundancies within these circuits and substantial cellular heterogeneity pose a major research challenge. We present CRISP-seq, an integrated method for massively parallel single-cell RNA-seq and CRISPR pooled screens. We show that profiling the perturbation and transcriptome in the same cell, enables to elucidate, the function of multiple factors and their interactions. In this benchmarking study, we applied this technology to probe regulatory circuits of innate immunity. By sampling tens of thousands of perturbed cells in vitro and in mice, we identified interactions and redundancies between developmental and signaling-dependent factors controlling the commitment toward different cell lineages or the inflammatory and antiviral pathways. CRISP-seq thereby emerges as a broadly applicable, comprehensive, and unbiased approach for elucidating mammalian regulatory circuits. Overall design: Transcriptional and CRISPR profiles from single myeloid cells, infected with lentiviral vectors carrying different gRNAs, were generated by deep sequencing of tens of thousands of single cells, sequenced in several batches in an Illumina Nextseq 500. Experiment was paired-end, but read2 was used to read cell and molecule barcodes only. Additional details about experimental design (associating each single cell with its amplification batch and index sorting readout) available as Series supplementary file.
Publication Title
Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Mus musculus
- 50 Downloadable Samples
- IlluminaHiSeq1500
Description
We develop a new ChIpseq method (iChIP) to profile chromatin states of low cell number samples. We use IChIP to profile the chromatin dynamics during hematopoiesis across 16 different cell types which include the principal hematopoietic progenitors Overall design: 3'' RNA-seq for digital gene expression quantitation across multiple cell types.
Publication Title
Immunogenetics. Chromatin state dynamics during blood formation.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- NextSeq 500
Description
Single cell RNA sequencing of murine circulating blood monocytes under steady state conditions. 2 plates of cx3cr1-cre:rosa26YFP monocytes and 4 plates (3 plates total monocytes and 1 plate Ly6Cint monocytes) were pre-enriched by CD115-biotin MACS and afterwards FACS sorted. Overall design: Indexed FACS sorting in 384well plates followed by MARS-Seq (Jaitin et al., Science 2014).
Publication Title
Genomic Characterization of Murine Monocytes Reveals C/EBPβ Transcription Factor Dependence of Ly6C<sup>-</sup> Cells.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Subject
View Samples- Mus musculus
- 54 Downloadable Samples
- NextSeq 500
Description
Within the bone marrow, hematopoietic stem cells differentiate and give rise to diverse blood cell types and functions. Currently, hematopoietic progenitors are defined using surface markers combined with functional assays that are not directly linked with the in vivo potential or gene regulatory mechanisms. Here we comprehensively identify myeloid progenitor subpopulations by transcriptional sorting of single cells from the bone marrow. We describe multiple progenitor subgroups showing unexpected transcriptional priming towards seven differentiation fates, but no progenitors with a mixed state. Transcriptional differentiation is correlated with combinations of known and previously undefined transcription factors, suggesting the process is tightly regulated. Histone maps and knockout assays are consistent with the transcriptional states while traditional transplantation experiments are only partially overlapping myeloid transcriptional priming. Our analyses uncover the function of the underlying regulatory mechanisms for several sub groups and establishes a general framework for dissecting hematopoiesis. Overall design: Bone marrow Lin- cKit+ Sca1- myeloid progenitors mRNA profiles from single cells were generated by deep sequencing of thousands of single cells, sequenced in several batches in an Illumina NextSeq Please note that [1] raw data files were processed as single-ended file since second read (mate) files contain only cell/molecule barcodes and therefore, not provided. This information was appended to the fastq entry header [2] The ''experimental_design.txt'' file explains the correspondence of each single cell (WXXXX) in the ''umitab.txt'' to a sample (ABXXXX).
Publication Title
Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Mus musculus
- 46 Downloadable Samples
- NextSeq 500
Description
Innate lymphoid cells (ILCs) are critical modulators of mucosal immunity, inflammation, and tissue homeostasis, but their full spectrum of cellular states and regulatory landscapes remain elusive. Here, we use a combination of genome-wide RNA-seq, ChIP-seq and ATAC-seq to compare the transcriptional and epigenetic identity of small intestinal ILCs, identifying thousands of distinct gene profiles and regulatory elements. Single-cell RNA-seq, cytometry, and imaging analyses reveal functional compartmentalization of cytokine expression and metabolic activity within the three classical ILC subtypes, and highlight transcriptional states beyond the current canonical classification. In addition, using antibiotic intervention and germ-free mice, we characterize the effect of the microbiome on the ILC regulatory landscape, and determine the response of ILCs to microbial colonization at the single-cell level. Together, our work characterizes the spectrum of transcriptional identities of small intestinal ILCs and describes how ILCs differentially integrate signals from the microbial microenvironment to generate phenotypic and functional plasticity. Overall design: ILC1(CD45+CD3-CD19-GR1-B220-CD127+ROR?t-NkP46+), ILC2(CD45+CD3-CD19-GR1-B220-CD127+ROR?t-KLRG1+) and ILC3(CD45+CD3-CD19-GR1-B220-CD127+ROR?t+) were isolated from small intestine lamina propria of WT C57Bl/6 ROR?t-GFP mice, or antibiotics treated mice (vancomycin, ampicillin,kanamycin, and metronidazole)
Publication Title
The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Corrigendum: Deterministic direct reprogramming of somatic cells to pluripotency.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Somatic cells can be directly reprogrammed to pluripotency by exogenous expression of transcription factors, classically Oct4, Sox2, Klf4 and c-Myc. While distinct types of somatic cells can be reprogramed with varying efficiencies and by different modified reprogramming protocols, induced pluripotent stem cell (iPSC) induction remains inefficient and stochastic where a fraction of the cells converts into iPSCs. The nature of rate limiting barrier(s) preventing majority of cells to convert into iPSCs remains elusive. Here we show that neutralizing Mbd3, a core member of the Mbd3/NURD co-repressor and chromatin-remodeling complex, results in deterministic and synchronized reprogramming of multiple differentiated cell types to pluripotency. 100% of Mbd3 depleted mouse and human somatic cells convert into iPSCs after seven days of reprogramming factor induction. Our findings delineate a critical pathway blocking the reestablishment of pluripotency, and offer a novel platform for future dissection of epigenetic dynamics leading to iPSC formation at high resolution.
Publication Title
Deterministic direct reprogramming of somatic cells to pluripotency.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 89 Downloadable Samples
- NextSeq 500
Description
Alzheimer''s disease (AD) is a detrimental neurodegenerative disease with no effective treatments. Due to cellular heterogeneity, the roles of immune cell subsets in AD onset and progression are poorly understood. By transcriptional single cell sorting, we comprehensively map all immune populations in wild type and AD–transgenic (Tg-AD) mouse brains. We describe a novel microglia type associated with neurodegenerative diseases (DAM) and identify the markers, spatial-location, and pathways associated with these cells. Immunohistochemical staining of mice and human brain slices showed DAM with intracellular/phagocytic Aß particles. Single cell analysis of DAM in Tg-AD and Trem2-/- Tg-AD revealed that the DAM program is activated in a two-step process. Activation is initiated in a Trem2 independent manner which involves down-regulation of microglia checkpoints, followed by activation of a Trem2-dependent program. These data identify a unique microglia-type, which may have important implications for future treatment of AD and other neurodegenerative diseases. Overall design: Transcriptional profiling of single cells from immune populations of mouse models of neurodegenerative diseases with matched controls, generated from deep sequencing of tens of thousands of cells, sequenced in several batches on illumina Nextseq500
Publication Title
A Unique Microglia Type Associated with Restricting Development of Alzheimer's Disease.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Mus musculus
- 83 Downloadable Samples
- NextSeq 500
Description
Microglia play important roles in life-long brain maintenance and in pathology, but are also crucial in the developing central nervous system; yet their regulatory dynamics during development have not been fully elucidated. Genome-wide chromatin and expression profiling coupled with single-cell transcriptomic analysis throughout development reveal that microglia undergo three temporal developmental stages in synchrony with the brain: early, pre-, and adult microglia, which are under the control of distinct regulatory circuits. Knockout of the transcription factor MafB caused disruption of homeostasis in adulthood and increased inflammation. Environmental perturbations, such as the microbiome or prenatal immune activation, led to dysregulation of the developmental program, particularly in terms of inflammation. Together, our work identifies a stepwise developmental program of microglia integrating immune response pathways that may be associated with several neurodevelopmental disorders. Overall design: Yolk sac progenitors (CD45+CD11B+CX3CR1-GFP+), microglia from early brain (CD45+CD11B+CX3CR1-GFP+), and microglia from later stages (CD45intCD11BintCX3CR1-GFP+) were isolated from CX3CR1+ C57BL/6J mice or microglia from perturbation models (CD45intCD11Bint) from mice of C57BL/6J background
Publication Title
Microglia development follows a stepwise program to regulate brain homeostasis.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Drosophila melanogaster
- 18 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Heterochromatin protein 1a (HP1a) is a chromatin associated protein that has been well studied in many model organisms, such as Drosophila, where it is a determining factor for classical heterochromatin. HP1a is associated with the two histone methyltransferases SETDB1 and Su(var)3-9, which mediate H3K9 methylation marks and participate in the establishment and spreading of HP1a enriched chromatin. While HP1a is generally regarded as a factor that represses gene transcription, several reports have linked HP1a binding to active genes, and in some cases, it has been shown to stimulate transcriptional activity. To clarify the function of HP1a in transcription regulation and its association with Su(var)3-9, SETDB1 and the chromosome 4 specific protein POF, we conducted genome-wide expression studies and combined the results with available binding data in Drosophila melanogaster. The results suggested that HP1a has a repressing function on chromosome 4, where it preferentially targets non-ubiquitously expressed genes (NUEGs), and a stimulating function in pericentromeric regions. Further, we showed that the effects of SETDB1 and Su(var)3-9 are similar to HP1a, and on chromosome 4, Su(var)3-9, SETDB1 and HP1a target the same genes. In contrast, transposons are repressed by HP1a and Su(var)3-9 but are un-affected by SETDB1 and POF. In addition, we found that the binding level and expression effects of HP1a are affected by gene length. Our results indicate that genes have adapted to be properly expressed in their local chromatin environment.
Publication Title
HP1a, Su(var)3-9, SETDB1 and POF stimulate or repress gene expression depending on genomic position, gene length and expression pattern in Drosophila melanogaster.
Sample Metadata Fields
No sample metadata fields
View Samples