Projects initiated and funded by the CESCG

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Legend:

- Plate-based sequencing (e.g. SMART-seq2)

- - Droplet-based sequencing (e.g. 10X) + + - Droplet-based sequencing (e.g. 10X)

- Online Data Archive (e.g. GEO)

- PubMed Link

- SC Hub File Download

- SC Hub Metadata Download

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- - - - + + + - - - - - - - - - + + + + + + + + + - + - + - - - + + + + spatial transcriptomics where flourescent probes are used to + measure both the relative expression of specific genes and where + these genes are being activated." + data-content="Click info icon to read the Spatial Transcriptomics paper (2016)."> + + Imaging + + + - - - - + + + + - - - - + + + - - + + data-container="body" data-html="true" + title="" + data-content="Using iPSC-based models and neurosphere RNA-seq data to study autism + spectrum disorder."> +
+ + + + + + + + + + + + + - + - + - - + - + + + - + - - - + - + data-toggle="popover" data-trigger="hover" class="popoveradjust" + data-placement="top" data-container="body" data-html="true" + title="Pollen AA et al. 2019. Establishing Cerebral Organoids as Models of + Human-Specific Brain Evolution. Cell." + data-content="View publication from this dataset"> + + + + + + - + - - - + - + target="_blank" + data-toggle="popover" data-trigger="hover" class="popoveradjust" + data-placement="top" data-container="body" data-html="true" + title="" + data-content="Download from the Stem Cell Hub"> + + + - + - - + - + target="_blank" + data-toggle="popover" data-trigger="hover" class="popoveradjust" + data-placement="top" data-container="body" data-html="true" + title="" + data-content="Download from the Stem Cell Hub"> + + + - + - + + --> - - + - + - + - - + + + - + - - + + and neurodegeneration."> + - + - - + + derived cardiomyocytes at four stages of differentiation."> + - + - - + dosage at single cell resolution in iPSC-derived cardiomyocytes."> + + - + - - - - + functional cardiomyocytes for cardiac and vascular regenerative repairs.">Chi + + + + - + - - + + - + - - - + - + - + - + - - - + towards cardiomyocytes.">Jones + + + - + - - + + - - - - + + - + - + - - - + + iPSC lines."> + - + - - + + + - + - + - + + - + - + - + - - + + - + - - - + + + - + - + - + - - - - + - + data-placement="top" data-container="body" data-html="true" + title="" + data-content="Single-cell RNA-seq of the rare, blood-forming haematopoietic + stem cells (HSCs) in bone marrow. Bone marrow cells were separated using FACS + with sorting on standard, in-house developed markers."> + + - + - + - + the mouse.">Belmonte + + + - + - - - - - - + + + + + + + - + - - + + - + - - + contributes to the regulation of gene expression and protein diversity.">Sanford + + + - + - + - - + - + - + - - - + + - - + + + - + - +

Research Theme	Lab	Data Set	Single cell + Research Theme +	+ Lab +	+ Data Set +	+ Single cell +	WGS	Amplicon-seq	- RNA-seq	Capture-seq	Frac-seq	broad-ChIP-seq	narrow-ChIP-seq	TCL-seq	+ +	+ + + + + WGS + + +	+ + + + + Amplicon-seq + + +	+ + + + + RNA-seq + + +	+ + + + + Capture-seq + + +	+ + + + + Frac-seq + + +	+ + + + + broad-ChIP-seq + + +	+ + + + + narrow-ChIP-seq + + +	+ + + WGBS
									Histone modification			Methylome		Chromatin modeling		Gene editing profiling	+ Histone modification +			+ Methylome +		+ Chromatin modeling +	+ Gene editing profiling +
				Genomics		Transcriptomics			Epigenomics
Neurobiology
Neurobiology
	Geschwind / + Pasca -	geschwindNeurospheres1 - Geschwind + + / Pasca + +	+ geschwindNeurospheres1 +			+ +			+ +
	+ Kriegstein -	kriegsteinBrainOrganoids1 + +	+ kriegsteinBrainOrganoids1 + + + - + data-toggle="popover" data-trigger="hover" class="popoveradjust" + data-placement="top" data-container="body" data-html="true" + title="Pollen AA et al. 2019. Establishing Cerebral Organoids as Models of + Human-Specific Brain Evolution. Cell." + data-content="View publication from this dataset"> + + + + + -		+ +				+ +
	-	kriegsteinBrainOrganoids2 +		+ kriegsteinBrainOrganoids2 + + -		+ +				+ +
		kriegsteinRadialGliaStudy1 +		+ kriegsteinRadialGliaStudy1 + + + - + data-toggle="popover" data-trigger="hover" class="popoveradjust" + data-placement="top" data-container="body" data-html="true" + title="Pollen AA et al. 2015. Molecular identity of human outer radial glia + during cortical development. Cell." + data-content="View publication from this dataset"> + + + + +		+ +				+ +
		kriegstein6k +		+ kriegstein6k + + + - + data-toggle="popover" data-trigger="hover" class="popoveradjust" + data-placement="top" data-container="body" data-html="true" + title="Nowakowski TJ et al. 2017. Spatiotemporal gene expression trajectories reveal + developmental hierarchies of the human cortex. Science." + data-content="View publication from this dataset"> + + + + +		+ +				+ +
	+ Quake	quakeBrainGeo1 + mechanisms of pathogenesis.">Quake + +	+ quakeBrainGeo1 - + data-toggle="popover" data-trigger="hover" class="popoveradjust" + data-placement="top" data-container="body" data-html="true" + title="" + data-content="Examination of cell types in healthy human brain samples."> + - + data-toggle="popover" data-trigger="hover" class="popoveradjust" + data-placement="top" data-container="body" data-html="true" + title="Darmanis S et al. 2015. A survey of human brain transcriptome + diversity at the single cell level. PNAS." + data-content="View publication from this dataset"> + + + + +		+ +				+ +
		quakeGlioblastomaGeo1 +	+ quakeGlioblastomaGeo1 + + - + data-toggle="popover" data-trigger="hover" class="popoveradjust" + data-placement="top" data-container="body" data-html="true" + title="Darmanis, S., et al. (2017). Single-Cell RNA-Seq Analysis of + Infiltrating Neoplastic Cells at the Migrating Front of Human + Glioblastoma. Cell Rep." + data-content="View publication from this dataset"> + + + + + -		+ +				+ +
	+ Yeo -	yeoRnaLocalization1 +	+ yeoRnaLocalization1 +					+ +
Cardiac biology
	+ Bruneau	bruneauCardioEpigenetics1	+ bruneauCardioEpigenetics1 +								+ +
		bruneauTbx5		+ +				+ +
	+ Chi	chiCardiomyocyte1		+ chiCardiomyocyte1 + +	+ +				+ +
		chiMouseCardiomyocyte		+ chiMouseCardiomyocyte + +	+ +				+ +
	+ Frazer	frazerCardIps1	+ frazerCardIps1 + +					+ +				+ +						+ +
	+ Jones	jonesYap1	+ jonesYap1 + +					+ +					+ +	+ +
	Snyder / Wu	snyderCardIps1	+ Snyder + + / Wu + +	+ snyderCardIps1 + +			+ +			+ +
Blood stem cells
	+ Baldwin -	baldwin12PairedIpscCellLines1 +	+ baldwin12PairedIpscCellLines1 +			+ +
	+ Corn -	cornErythroidMaturation + +	+ cornErythroidMaturation + + + -					+ +											+ +
		cornOffTarget +	+ cornOffTarget + + + -				+ +			+ +										+ +
		cornHSPC		+ cornHSPC + +	+ +				+ +
	+ Crooks -	crooksHsc	+ crooksHsc + +					+ +				+ +						+ +
	Weissman -	weissmanHcs1	+ weissmanHcs1 +		+ +				+ +
Molecular regulators of stem cells	Molecular regulators of stem cells
	Belmonte	belmonteMouseDnmt3a	+ belmonteMouseDnmt3a + +					+ +
	+ Fan -	fanIcf1					+ fanIcf1 + +	+ +	+ +	+ +	+ +				+ +					+ +	+ +		+ +
	+ Sanford	sanfordRnaRegulation1	+ sanfordRnaRegulation1 + +					+ +			+ +
Pancreas
	Quake	quakePancreas1 - + data-placement="top" data-container="body" data-html="true" + title="Stephen Quake, Stanford University" + data-content="The Quake lab is working on characterizing cell subpopulations + of healthy and pathological tissues of the brain and pancreas. They are also + looking at gene and epigenetic properties of organ lineages to compare stem + cell differentiation hierarchy to normal tissues to elucidate mechanisms of + pathogenesis.">Quake + +	+ quakePancreas1 + + + - + data-toggle="popover" data-trigger="hover" class="popoveradjust" + data-placement="top" data-container="body" data-html="true" + title="Enge M et al. 2017. Single-Cell Analysis of Human Pancreas Reveals + Transcriptional Signatures of Aging and Somatic Mutation Pattern. Cell." + data-content="View publication from this dataset"> + + + + +		+ +				+ +
		quakeFetalPancreasSpatial -	+ quakeFetalPancreasSpatial + + - + data-toggle="popover" data-trigger="hover" class="popoveradjust" + data-placement="top" data-container="body" data-html="true" + title="Riu L et al. 2019. Modeling Spatial Correlation of Transcripts + with Application to Developing Pancreas. Nat Sci Rep." + data-content="View publication from this dataset"> + +																+ +
Therapeutics
	+ Loring -	loringParkinsons1	+ loringParkinsons1 + +			+ +			+ +