Tabula Sapiens v2 update

datasets/tabula-sapiens.yaml

@@ -1,24 +1,45 @@
 Name: Tabula Sapiens
 Description: |
-  Tabula Sapiens will be a benchmark, first-draft human cell atlas of two million cells from 25 organs of eight normal human subjects. 
-  Taking the organs from the same individual controls for genetic background, age, environment, and epigenetic effects, and allows detailed analysis and comparison of cell types that are shared between tissues. 
-  Our work creates a detailed portrait of cell types as well as their distribution and variation in gene expression across tissues and within the endothelial, epithelial, stromal and immune compartments. 
-  A critical factor in the Tabula projects is our large collaborative network of PI’s with deep expertise at preparation of diverse organs, enabling all organs from a subject to be successfully processed within a single day. 
-  Tabula Sapiens leverages our network of human tissue experts and a close collaboration with a Donor Network West, a not-for-profit organ procurement organization. 
-  We use their experience to balance and assign cell types from each tissue compartment and optimally mix high-quality plate-seq data and high-volume droplet-based data to provide a broad and deep benchmark atlas. 
-  Our goal is to make sequence data rapidly and broadly available to the scientific community as a community resource. Before you use our data, please take note of our Data Release Policy below.</br></br>
+  Tabula Sapiens is a benchmark, first-draft human cell atlas of over 1.1M cells from 28 organs of 24 normal human subjects. 
+  This work is the product of the Tabula Sapiens Consortium. 
+  Taking the organs from the same individual controls for genetic background, age, environment, and epigenetic effects, 
+  and allows detailed analysis and comparison of cell types that are shared between tissues. 
+  Our work creates a detailed portrait of cell types as well as their distribution and variation in gene expression 
+  across tissues and within the endothelial, epithelial, stromal and immune compartments.
+  We have built directly on our unique skills, experience, and data infrastructure from Tabula Muris and Tabula Muris Senis 
+  to create a high-quality human reference dataset and portal at a 10-fold larger scale from these prior efforts.
 
-  Data Release Policy</br></br>
+  A critical factor in the Tabula projects is our large collaborative network of PIs with deep expertise at preparation of diverse organs, 
+  enabling all organs from a subject to be successfully processed within a single day. 
+  We have built the logistics and infrastructure capable of tracking hundreds of samples and thousands of 384-well plates 
+  from tissue through sample prep, library construction and on to sequencing and ultimately computational 
+  and expert cell annotation with tight quality control.
+
+  Tabula Sapiens leverages our network of human tissue experts and a close collaboration with a Donor Network West, 
+  a not-for-profit organ procurement organization. We use their experience to balance and assign cell types 
+  from each tissue compartment and optimally mix high-quality plate-seq data and high-volume droplet-based data to 
+  provide a broad and deep benchmark atlas.
+
+  The first version of Tabula Sapiens contained nearly 500,000 cells from 24 organs of 15 normal human subjects.
+  With the second version, Tabula Sapiens 2.0, we have built an integrated map of 28 tissues collected across 24 donors. 
+  Nine new donors and four new tissues were collected and analyzed together with the original Tabula Sapiens 1.0 dataset. 
+  All tissues and organs, with the exception of the respective reproductive organs, were profiled from both male (n=11) and female (n=13) donors. 
+  The donor's age ranges from 22 to 74 years old, offering one of the most comprehensive molecular profiles of human tissues across the 
+  adult lifespan (7 donors under the age of 40, 11 donors between 40 and 60, and 6 donors over 60 years of age).
 
-  Our goal is to make sequence data rapidly and broadly available to the scientific community as a community resource. It is our intention to publish the work of this project in a timely fashion, and we welcome collaborative interaction on the project and analyses. 
-  However, considerable investment was made in generating these data and we ask that you respect rights of first publication and acknowledgment as outlined in the [Toronto agreement](https://www.nature.com/articles/461168a). 
-  By accessing these data, you agree not to publish any articles containing analyses of genes, cell types or transcriptomic data on a whole atlas or tissue scale prior to initial publication by the Tabula Sapiens Consortium and its collaborating scientists. 
-  If you wish to make use of restricted data for publication or are interested in collaborating on the analyses of these data, please use email or contact form available from the portal. 
-  Redistribution of these data should include the full text of the data use policy.
-Documentation: http://tabula-sapiens-portal.ds.czbiohub.org/
-Contact: https://github.com/czbiohub/tabula-muris-senis/issues
+  Our goal is to make sequence data rapidly and broadly available to the scientific community as a community resource and 
+  we welcome collaborative interaction on the project and analyses. By accessing these data, you agree to cite our work as 
+  The Tabula Sapiens Consortium, Science 376, eabl4896 (2022) if using the original v1 dataset, or to cite our 
+  work as The Tabula Sapiens Consortium, biorxiv (2024) if you are using the Tabula Sapiens v2 data release. 
+  All processed data is available (see below) and the raw data is browsable from AWS. Redistribution of these data should 
+  include the full text of the data use policy.
+
+  If you wish to gain access to the raw fastq files, please submit a request using the controlled access form to sign the data use agreement, 
+  upon which we may grant you access to the files. Raw fastq files should not be transferred to any third party.
+Documentation: https://tabula-sapiens.sf.czbiohub.org/
+Contact: [email protected], [email protected]
 ManagedBy: "[Chan Zuckerberg Biohub](https://www.czbiohub.org/)"
-UpdateFrequency: This is the first version of the dataset and it will be updated once per month until project completion.
+UpdateFrequency: This is the second version of the dataset. We expect to update every 1-2 years until project completion.
 Tags:
   - aws-pds
   - biology
@@ -29,15 +50,18 @@ Tags:
   - life sciences
   - medicine
   - single-cell transcriptomics
-License: http://tabula-sapiens-portal.ds.czbiohub.org/whereisthedata
+License: https://tabula-sapiens.sf.czbiohub.org/whereisthedata
 Resources:
-  - Description: http://tabula-sapiens-portal.ds.czbiohub.org
+  - Description: https://tabula-sapiens.sf.czbiohub.org/about
     ARN: arn:aws:s3:::czb-tabula-sapiens
     Region: us-west-2
     Type: S3 Bucket
-    ControlledAccess: https://docs.google.com/forms/d/e/1FAIpQLSeeB0N7TrklXbCbpc6nDi5e77uad3uZDZ4WCMV77jwhVzxUtQ/viewform
+    ControlledAccess: https://us.services.docusign.net/webforms-ux/v1.0/forms/a6c0eb9af42c45ce9ed78a1292f56dab
 DataAtWork:
   Publications:
     - Title: "The Tabula Sapiens: a multiple organ single cell transcriptomic atlas of humans"
       URL: https://www.science.org/doi/10.1126/science.abl4896
-      AuthorName: The Tabula Sapiens Consortium, Stephen R Quake
+      AuthorName: The Tabula Sapiens Consortium
+    - Title: "Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues"
+      URL: https://www.biorxiv.org/content/10.1101/2024.12.03.626516v1
+      AuthorName: The Tabula Sapiens Consortium, Stephen R Quake