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2022-Strand et al-Cancer Cell

PostPosted: Thu Dec 15, 2022 5:44 pm
by mleipold
"Molecular classification and biomarkers of clinical outcome in breast ductal carcinoma in situ: Analysis of TBCRC 038 and RAHBT cohorts"
Siri H Strand, Belén Rivero-Gutiérrez, Kathleen E Houlahan, Jose A Seoane, Lorraine M King, Tyler Risom, Lunden A Simpson, Sujay Vennam, Aziz Khan, Luis Cisneros, Timothy Hardman, Bryan Harmon, Fergus Couch, Kristalyn Gallagher, Mark Kilgore, Shi Wei, Angela DeMichele, Tari King, Priscilla F McAuliffe, Julie Nangia, Joanna Lee, Jennifer Tseng, Anna Maria Storniolo, Alastair M Thompson, Gaorav P Gupta, Robyn Burns, Deborah J Veis, Katherine DeSchryver, Chunfang Zhu, Magdalena Matusiak, Jason Wang, Shirley X Zhu, Jen Tappenden, Daisy Yi Ding, Dadong Zhang, Jingqin Luo, Shu Jiang, Sushama Varma, Lauren Anderson, Cody Straub, Sucheta Srivastava, Christina Curtis, Rob Tibshirani, Robert Michael Angelo, Allison Hall, Kouros Owzar, Kornelia Polyak, Carlo Maley, Jeffrey R Marks, Graham A Colditz, E Shelley Hwang, Robert B West
Cancer Cell. 2022

From STAR Methods table:
- "RAHBT MIBI imaging data: (Atlas name: HTAN Duke)"
- "
Data Download
The HTAN Portal leverages several data repositories to provide download of data:

Synapse - Dowload processed level 3 and level 4 data
dbGaP - Download Level 1 & 2 sequencing data
Imaging Data Commons (IDC) - Download imaging data in DICOM-TIFF format"

The Synapse link is the only one where I can find "MIBI" or "HTAN Duke". Unfortunately, both are currently greyed out with 0 files.

- "Data and code availability RNA and DNA sequencing data, metadata, and MIBI and H&E imaging data, have been deposited at the HTAN portal and are publicly available as of the date of publication (HTAN portal: ... 2371.v1.p1). For further information see the key resources table."
- this only leads to dbGaP sequencing data; no MIBI.