Similar studies for GEO DataSets (Select 200061470) - GEO DataSets

Select item 2000614701.

Decoding the regulatory network of early blood development from single-cell gene expression measurements.

(Submitter supplied) Reconstruction of the molecular pathways controlling organ development has been hampered by a lack of methods to resolve embryonic progenitor cells. Here we describe a strategy to address this problem that combines gene expression profiling of large numbers of single cells with data analysis based on diffusion maps for dimensionality reduction and network synthesis from state transition graphs. Applying the approach to hematopoietic development in the mouse embryo, we map the progression of mesoderm toward blood using single-cell gene expression analysis of 3,934 cells with blood-forming potential captured at four time points between E7.0 and E8.5. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
15 Samples

Download data: XLS

Series

Accession:: GSE61470

ID:: 200061470

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001366892.

Single cell sequencing of dissected mouse foreguts at embryonic day 8.5 to 9.5

(Submitter supplied) Single cell sequencing of dissected mouse foreguts at embryonic day 8.5 to 9.5

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
4 Samples

Download data: TXT

Series

Accession:: GSE136689

ID:: 200136689

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Select item 2001366873.

Transcriptomic changes in the mouse foregut comparing Gli2,3 double mutant to heterozygous controls

(Submitter supplied) We dissected foreguts from Gli2-/-,Gli3-/- and Gli2+/-,Gli3+/- mouse embryos at embryonic day 9.5. Three foreguts were obtained for each group and each foregut was individually processed for bulk RNA extraction and library preparation. Sequencing results identified Gli positively and negatively regulated genes in the foreguts.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
6 Samples

Download data: XLSX

Series

Accession:: GSE136687

ID:: 200136687

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000789074.

Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (single cell RNA Seq of Gfi1-/- Irf8-/- GMP)

(Submitter supplied) Single cell RNA seq and bioinformatic analysis is used to characterize myeloid differentiation to uncover novel transcriptional networks and key drivers of hematoipoietic development

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
47 Samples

Download data: TXT

Series

Accession:: GSE78907

ID:: 200078907

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000702455.

Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL17021
680 Samples

Download data: TSV, TXT

Series

Accession:: GSE70245

ID:: 200070245

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Select item 2000702446.

Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (single cell RNA Seq of bone marrow lineage-negative Sca1+ CD117+ cells)

(Submitter supplied) Single cell RNA seq and bioinformatic analysis is used to characterize myeloid differentiation to uncover novel transcriptional networks and key drivers of hematoipoietic development

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
96 Samples

Download data: TXT

Series

Accession:: GSE70244

ID:: 200070244

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000702437.

Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (single cell RNA Seq of bone marrow lineage-negative CD117+ CD34+ cells)

(Submitter supplied) Single cell RNA seq and bioinformatic analysis is used to characterize myeloid differentiation to uncover novel transcriptional networks and key drivers of hematoipoietic development

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
66 Samples

Download data: TXT

Series

Accession:: GSE70243

ID:: 200070243

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000702428.

Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (single cell RNA Seq of Irf8 KO GMP)

(Submitter supplied) Single cell RNA seq and bioinformatic analysis is used to characterize myeloid differentiation to uncover novel transcriptional networks and key drivers of hematoipoietic development

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
63 Samples

Download data: TXT

Series

Accession:: GSE70242

ID:: 200070242

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000702419.

Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (single cell RNA Seq of Irf8-GFP GMP)

(Submitter supplied) Single cell RNA seq and bioinformatic analysis is used to characterize myeloid differentiation to uncover novel transcriptional networks and key drivers of hematoipoietic development

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
37 Samples

Download data: TXT

Series

Accession:: GSE70241

ID:: 200070241

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20007024010.

Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (single cell RNA Seq of GMP)

(Submitter supplied) Single cell RNA seq and bioinformatic analysis is used to characterize myeloid differentiation to uncover novel transcriptional networks and key drivers of hematoipoietic development

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
136 Samples

Download data: TXT

Series

Accession:: GSE70240

ID:: 200070240

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20007023911.

Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (single cell RNA Seq of Gfi1-/- GMP)

(Submitter supplied) Single cell RNA seq and bioinformatic analysis is used to characterize myeloid differentiation to uncover novel transcriptional networks and key drivers of hematoipoietic development

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
80 Samples

Download data: TXT

Series

Accession:: GSE70239

ID:: 200070239

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20007023812.

Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (single cell RNA Seq of Gfi1-GFP GMP)

(Submitter supplied) Single cell RNA seq and bioinformatic analysis is used to characterize myeloid differentiation to uncover novel transcriptional networks and key drivers of hematoipoietic development

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
39 Samples

Download data: TXT

Series

Accession:: GSE70238

ID:: 200070238

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20007023713.

Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (ChIP-seq)

(Submitter supplied) Single cell RNA seq and bioinformatic analysis is used to characterize myeloid differentiation to uncover novel transcriptional networks and key drivers of hematopoietic development

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL17021
5 Samples

Download data: TSV, TXT

Series

Accession:: GSE70237

ID:: 200070237

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20007023614.

Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (single cell RNA Seq from CMP)

(Submitter supplied) Single cell RNA seq and bioinformatic analysis is used to characterize myeloid differentiation to uncover novel transcriptional networks and key drivers of hematoipoietic development

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
96 Samples

Download data: TXT

Series

Accession:: GSE70236

ID:: 200070236

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20007023515.

Using single-cell RNA-Seq for unbiased analysis of developmental hierarchies (Bulk RNA-Seq)

(Submitter supplied) Single cell RNA seq and bioinformatic analysis is used to characterize myeloid differentiation to uncover novel transcriptional networks and key drivers of hematopoietic development

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
15 Samples

Download data: TXT

Series

Accession:: GSE70235

ID:: 200070235

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20006977616.

A fully validated blood stem/progenitor cell regulatory network reveals mechanisms of cell state stabilisation

(Submitter supplied) The aim of this study was to determine the genomic binding sites of important haematopoietic transcription factors in haematopoietic cell lines.

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL17021
11 Samples

Download data: BED, BW

Series

Accession:: GSE69776

ID:: 200069776

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20012516217.

Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments

(Submitter supplied) Understanding how gene expression programs are controlled requires identifying regulatory relationships between transcription factors and target genes. Gene regulatory networks are typically constructed from gene expression data acquired following genetic perturbation or environmental stimulus. Single-cell RNA sequencing (scRNAseq) captures the gene expression state of thousands of individual cells in a single experiment, offering advantages in combinatorial experimental design, large numbers of independent measurements, and accessing the interaction between the cell cycle and environmental responses that is hidden by population-level analysis of gene expression. more...

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by high throughput sequencing

Platform:: GPL19756
12 Samples

Download data: MTX, TSV

Series

Accession:: GSE125162

ID:: 200125162

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20011455718.

cisTopic: cis-regulatory topic modelling on single-cell ATAC-seq data

(Submitter supplied) We present cisTopic, a probabilistic framework to simultaneously discover co-accessible enhancers and stable cell states from sparse single-cell epigenomics data (http://github.com/aertslab/cistopic). On a compendium of single-cell ATAC-seq datasets from differentiating hematopoietic cells, brain, and transcription-factor perturbation dynamics, we demonstrate that topic modelling can be exploited for a robust identification of cell types, enhancers, and relevant transcription factors. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms
771 Samples

Download data: BW, NARROWPEAK, TXT

Series

Accession:: GSE114557

ID:: 200114557

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20016921019.

A single embryo, single cell time-resolved model for mouse gastrulation

(Submitter supplied) Mouse embryonic development is a canonical model system for studying mammalian cell fate acquisition. Recently, single-cell atlases comprehensively charted embryonic transcriptional landscapes, yet inference of the coordinated dynamics of cells over such atlases remains challenging. Here we introduce a temporal model for mouse gastrulation, consisting of data from 153 individually sampled embryos spanning 36 hours of molecular diversification. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL24247 GPL19057
154 Samples

Download data: TXT

Series

Accession:: GSE169210

ID:: 200169210

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20004251820.

High-throughput single cell gene expression analysis in primary blood stem and progenitor cells identifies new links between key transcriptional regulators

(Submitter supplied) Cellular decision-making is mediated by a complex interplay of external stimuli with the intracellular environment, in particular transcription factor regulatory networks. Here we have determined the expression of a network of 18 key haematopoietic transcription factors (TFs) in 597 single primary blood stem and progenitor cells isolated from mouse bone marrow. We demonstrate that different stem/progenitor populations are characterised by distinctive TF expression states, and through comprehensive bioinformatic analysis reveal positively and negatively correlated TF pairings, including previously unrecognised relationships between Gata2, Gfi1 and Gfi1b. more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL13112
2 Samples

Download data: BEDGRAPH

Series

Accession:: GSE42518

ID:: 200042518

PubMed Full text in PMC Similar studies SRA Run Selector

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