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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:
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- 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.'; - echo 'Contact the data wranglers using the form below to request access to our secure site, or to ask a question. We look forward to working with you!
'; - - - } - if ($_POST["mail_submission"]) - { - $count = 0; - $email = $_POST['email']; - $domain = substr(strrchr($email, "@"), 1); - - /**************************************************** - | Magic regex to validate email. Not perfect. | - ****************************************************/ - function validateEmail($email) - { - return filter_var($email, FILTER_VALIDATE_EMAIL); - } - - /**************************************************** - | Check if domain has an MX record to see exists. | - ****************************************************/ - function validateDomain($domain) - { - return checkdnsrr($domain, 'MX'); - } - - /**************************************************** - | Now use together to see if email is legit | - ****************************************************/ - if (validateEmail($email) == TRUE) - { - echo ""; - } else { - $errorList[$count] = "Missing or invalid: email address"; - $emailErrorDesc1 = "This email address does not appear valid.
"; - $count++; - $emailError = "1"; - } - if (validateDomain($domain) == TRUE) - { - echo ""; - } else { - $errorList[$count] = "Missing or invalid: email domain name"; - $emailErrorDesc2 = "This email's domain name does not appear to be real.
"; - $count++; - $emailError = "1"; - } - - if (!$_POST["name"]) { $nameError = "1"; $errorList[$count] = "Missing or invalid: your name"; $count++; } - if (!$_POST["subject"]) { $subjectError = "1"; $errorList[$count] = "Missing or invalid: subject"; $count++; } - if (!$_POST["message"]) { $messageError = "1"; $errorList[$count] = "Missing or invalid: message"; $count++; } - - if (sizeof($errorList) == 0) - { - - /*-------------------------------------------------------------+ - | Make an email subject template. | - +-------------------------------------------------------------*/ - $subjectPackage = $_POST["subject"]." | CIRM CESCG DCM contact form"; - - /*---------------------------------------------------------+ - | Email template | - +---------------------------------------------------------*/ - $emailPackage = '------- -----------------------------------------------------------------------'; - $emailPackage .= "\n" .'From '.$_POST["name"].' <'.$_POST["email"].'> '; - $emailPackage .= "\n" .'------- -----------------------------------------------------------------------'; - $emailPackage .= "\n" .'Subject '.$subjectPackage; - $emailPackage .= "\n" .'--------------------------------------------------------------------------------'; - $emailPackage .= "\n" .'Message'; - $emailPackage .= "\n\n".$_POST["message"]; - $emailPackage .= "\n\n".'--------------------------------------------------------------------------------'; - - - /*-------------------------------------------------------------+ - | Setup Email Headers. | - +-------------------------------------------------------------*/ - $headers = 'Reply-To:'.$_POST["email"]."\r\n"; - if($rdType == 1) - { - $headers .= "MIME-Version: 1.0\n" . "Content-type: text/html; charset=iso-8859-1"; - $headers .= "X-mailer: soe.ucsc.edu" . "\r\n"; // this will identify the real sender - $headers.= "Precedence: bulk" . "\r\n"; // this will say it is bulk sender - $emailPackage = stripslashes($emailPackage); - } else { - $headers .= "MIME-Version: 1.0\n" . "Content-type: text/plain; charset=iso-8859-1"; - } - - #$emailto = "clmfisch@ucsc.edu"; - $emailto = "cirm-wrangler-group@ucsc.edu"; - /*-------------------------------------------------------------+ - | Send the Mail. | - +-------------------------------------------------------------*/ - $ok = @mail($emailto, $subjectPackage, $emailPackage, $headers); - - if ($ok) - { - /*---------------------------------------------------------+ - | Print out a template to show submission. | - +---------------------------------------------------------*/ - echo '".$emailPackage.""; - } else { - /*---------------------------------------------------------+ - | In the future, automatically send an error to me. | - +---------------------------------------------------------*/ - echo "
It seems the mail could not be sent, please try again.
"; - } - /*-----------------------------------------------------------------+ - | Errors were found - +-----------------------------------------------------------------*/ - } else { - echo '"; - } - */ - } - } - - if (!$ok) - { -?> -
Public files
-Here you can download all published, non-identifiable data.
- -Research themes
- - -Research Theme |
- Lab | -Data Set | -Single cell | -- | - | - | - | - | - | - | - | - | - | - | - | - - |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| - | - | - | - | 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
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