CESCG Organization Research Access Files Projects


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Welcome to the CIRM Genomics Hub, created from the Genomics Initiative from the California Institute for Regenerative Medicine's Center of Excellence for Stem Cell Genomics (CESCG).

The CESCG is made up of approximately 20 separate projects, all involving stem or progenitor cells. The first release of information explores single cell expression datasets in the human brain, tools to deconvolute complex mixtures of brain cells into cell types and developmental states, and scorecards for in vitro differentiation into brain subclasses.

CESCG: The CIRM Center of Excellence in Stem Cell Genomics

CIRM's goal in establishing the CESCG is to apply genomics and bioinformatics approaches to stem cell research to accelerate fundamental understanding of human biology and disease mechanisms, enhance cell and tissue production and advance personalized cellular therapeutics.

The CESCG is composed of Operational Cores at Stanford University and at the Salk Institute and a Data Coordination and Management Core at the University of California Santa Cruz, which currently support the following research programs:

1) Center-initiated Projects: Two projects are applying advanced genomics approaches, one to explore cardiac disease and drug toxicity and the other to investigate cell fate and identity. A third project is developing innovative bioinformatics tools to establish molecular network models and to guide predictions of cell fate.

2) Collaborative Research Program: Through the solicitation and participation in collaborative research projects, the CESCG provides stem cell scientists throughout the state of California with access to cutting-edge genomics and bioinformatics technologies, and expertise and assistance in experimental design and data analysis.

Components of CIRM's Genomics Initiative:

CIRM CESCG

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Data Coordination and Management Group (DCM)

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Data Curation Group (DCG)

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Research access to files requires additional authentication.

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Public files

Here you can download all published, non-identifiable data.

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Research themes


Research Theme		 Lab Data Set Single cell
WGS
Amplicon-seq
RNA-seq
Capture-seq
Frac-seq
broad-ChIP-seq
narrow-ChIP-seq
TCL-seq
WGBS
RRBS
ATAC-seq
Hi-C
GUIDE-seq
Histone modification Methylome Chromatin modeling Gene editing profiling
Genomics Transcriptomics Epigenomics
Neurobiology
Quake quakeBrainGeo1
quakeGlioblastomaGeo1
Kriegstein kriegsteinBrainOrganoids1
kriegsteinRadialGliaStudy1
Clarke
Yeo yeoRnaLocalization1
Geschwind geschwindNeurospheres1
Cardiac Biology
Frazer frazerCardIps1
Jones jonesYap1
Bruneau bruneauCardioEpigenetics1
Chi N/A
Snyder snyderCardIps1
Blood stem cells and therapeutics
Baldwin baldwin12PairedIpscCellLines1
Crooks crooksHsc
Loring loringParkinsons1
Weissman
Corn cornErythroidMaturation1
cornOffTarget
Molecular regulators of stem cells
Sanford sanfordRnaRegulation1
Fan fanIcf1
Belmonte belmonteMouseDnmt3a v

Single-cell Legend:

C1-based (SpeedSeq, SMART-seq2, CEL-seq)

Drop-seq

10X Genomics

Tag Storm

Metadata made simple

Tag Storms can utilize a suite of utilities.

SCIMITAR

Single Cell Inference of MorphIng Trajectories and their Associated Regulation

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5203771/

SCIMITAR can help scientists infer cell trajectory.

RIGGLE

Regulator Inference by Graph-Guided LASSO Estimation

MISCE

A Minimum Information About a Stem Cell Experiment

Single-cell brain analysis using RNA-seq reveals cellular heterogeneity - a community of cells that form the working brain

Help FAQ

Other CESCG resources

The CESCG is comprised of Operational Cores at Stanford University and the Salk Institute

Side panel

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Why do I need to request access to certain files?

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Why are some files not public?

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Informatics and neurobiology

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Cardiac biology

About 1% of all children are born with congenital heart defects

Blood stem cells and therapeutics

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Molecular regulators of stem cells

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Role of the DCM

Role of the DCG

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Why use RNA-seq?

RNA-seq is an assay scientists use to measure how often genes are being expressed, or turned off and on. With few exceptions, all cells in your body contain the same genome, yet are able to become the large variety of cells we see by changing how genes are expressed, leading to the community of cells we see.

Tools and scoreboard

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