Data Access Information

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TABLE OF CONTENTS

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• GENERAL INFORMATION
  • ASSOCIATED PUBLICATION
  • RECOMMENDED CITATION
  • USEFUL LINKS
• ACCESS THE DATASET
  • FILE ORGANIZATION
  • REPOSITORY LINKS
  • FILE LIST
• ADDITIONAL NOTES/COMMENTS ​

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GENERAL INFORMATION

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1. Publication or Dataset title: Clinical responses to trastuzumab deruxtecan in molecularly defined ependymoma
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2. Authors: L Nicolas Gonzalez Castro, Yi-Chien Wu, Jia-Ren Lin, Maria-Joao Santiago-Ribeiro, Alice Laurenge, Alexandre Carpentier, Shannon Coy, Nancy U. Lin, Karima Mokhtari, Keith L. Ligon, Mehdi Touat, Sandro Santagata ​

3. Please cite this data as the following:
   Gonzalez Castro (2026). Clinical responses to trastuzumab deruxtecan in molecularly defined ependymoma. {journal/biorxv}

4. Relevant links:

• Publication DOI: doi.org/MY-PAPER-DOI
• Associated GitHub Repository: MY-REPO
• To view an archived record of this repository: My-ZENODO-DOI
• To view the image data online, visit: My-ATLAS-PAGE

​ 5. Licenses/restrictions placed on the data: CC-BY creativecommons.org/licenses/by/4.0/ ​

ACCESS THE DATASET

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File organization:

Each file follows the following naming convention:
​ Each folder corresponds to a patient sample (N).

File Type	Description	Location
N.ome.tif	Stitched multiplex CyCIF image pyramid in ome.tif format	AWS
markers.csv	list of all markers in ome.tif image	Synapse
N.csv	single-cell feature table, including intensity data for all channels	Synapse
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AWS Data Access

​ X, Y, Z data is available for download through AWS. ​ You will need the following bucket name:

AWS BUCKET NAME  

​ For general instructions on how to download data from AWS, see: https://zenodo.org/records/10223574

If you experience issues accessing the above AWS S3 buckets, email tissue-atlas(at)hms.harvard.edu with the subject line "bucketname: Data Access".
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FILE LIST

Orion WSIs (19 channels)

Patient	Folder name	File name	File size (GB)
C1	CRC01	P37_S29_A24_C59kX_E15@20220106_014304_946511.ome.tiff	236.25
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markers.csv

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Patient or Biospecimen ID	File Name	Synapse ID	File size
ID	markers.csv	syn12345678	N.N bytes
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N.csv

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Patient or Biospecimen ID	File Name	Synapse ID	File size
ID	ID.csv
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ADDITIONAL NOTES/COMMENTS

​ Please let (Sandro Santagata, ssantagata@bwh.harvard.edu) know if any errors are found in this data.