SAIL’s experimental team is constantly optimizing and benchmarking single-cell and spatial genomics methods:
This protocol can be used for performing HCR Flow-FISH followed by cell/nuclei enrichment via FACS and polymer disassembly on fixed and permeabilized cells and tissue derived nuclei. This protocol should be performed after finalizing "PERFF-seq: Cell and Nuclei Preparation" for the desired sample type.
This protocol can be used for preparation of Cells and Fresh-Frozen and Formalin-Fixed Paraffin-Embedded (FFPE) Tissue Derived Nuclei. This protocol should be followed by "PERFF-seq: HCR-FlowFISH and Polymer Disassembly."
This protocol describes nuclei extraction from snap frozen tissue using Singulator, including washing nuclei suspension in buffer supplemented with sucrose, and nuclei FACS sorting. The resulting nuclei suspension is suitable for Single Cell Multiome ATAC + Gene Expression using 10x Chromium platform. The protocol has been validated on various healthy and cancer snap frozen human and mouse tissues (lung, brain, prostate, core needle biopsies etc) .
SAIL office hours
(1) Open for general MSKCC labs: Providing computational guidance / support on your own single-cell data analysis project (scRNA-seq, scATAC-seq).
Host: Roshan Sharma; Booking: here.
(2) Only open for labs with data generated by SAIL: Addressing your data access and data processing needs, sequence re-alignment etc.
Host: Tobias Krause; Booking: here.
Please note that we do not provide support for HPC or other IT related questions.
How to work with SAIL?
New collaborations and projects are discussed and initiated by contacting Ronan Chaligne (chalignr@mskcc.org) directly.
How to access my data?
IRIS, MSK's HPC cluster. We no longer use AWS S3 for routine data access — AWS is now used only for long-term archiving (data is moved to deep storage after 6 months).
To access your data on Iris, you'll need to be on the MSK network, signed in with your MSK credentials, and on an MSK machine. You can connect via Finder (Mac), File Explorer (Windows), or the terminal (Linux/Mac), and copy your data to your own Iris drive.
For full step-by-step instructions — including how to get access added through SailPoint and how to copy data — see our detailed guide:
Note: If you run into permissions issues, contact SAIL (Tobi – krauset@mskcc.org, or Matt – willm16@mskcc.org)
My data are archived! How can I access them anyway?
All data generated by SAIL and stored on AWS S3 is automatically archived in a lower-cost tier of storage called “AWS Glacier Deep Archive” after 6 months. If your data has been archived and you would like to retrieve it, you must submit an “AWS Glacier unarchiving” request on iLab. Once this request has been received, your files will temporarily be made available to download approximately 48 hours after receiving the request and will stay accessible for 30 days before being re-archived.