05/09/2024 | Press release | Distributed by Public on 05/09/2024 04:33
We are excited to share the second installment of tips for successful CosMx™ SMI single-cell spatial runs at 1000-plex. Our first installment of tips focused on data by tissue and disease type as well as tissue-specific sample preparation considerations, while our second installment focused on evaluating tissue block quality, section quality, heterogeneity, and autofluorescence. Here we focus on post-run H&E staining protocols.
The CosMx™ SMI and decoder probes are not offered and/or delivered to the Federal Republic of Germany for use in the Federal Republic of Germany for the detection of cellular RNA, messenger RNA, microRNA, ribosomal RNA and any combinations thereof in a method used in fluorescence in situ hybridization for detecting a plurality of analytes in a sample without the consent of the President and Fellows of Harvard College (Harvard Corporation) as owner of the German part of EP 2 794 928 B1. The use for the detection of cellular RNA, messenger RNA, microRNA, ribosomal RNA and any combinations thereof is prohibited without the consent of the President and Fellows of Harvard College (Harvard Corporation).
You will need the following materials and reagents for this step: staining jars, Xylene, razor blade, tape, Kimwipes, 2X SSC.
Flow cell removal involves the use of a razor blade and may result in broken glass. The blade and
glass present laceration hazards. Follow safety guidelines and wear proper PPE (e.g., hand protection, eye
protection, etc.) when performing this step. Dispose of sharps and glass appropriately following your
laboratory's safety policy.
Following the post-run clean, remove all flow cells to be imaged from the instrument and place into a staining jar containing Xylene. Leave flow cells in Xylene overnight at room temperature to loosen the flow cell adhesive and allow for easier coverslip removal.
The following day, take proper precautions and carefully remove the flow cell coverslip.
After removing the flow cell coverslip, remove the remaining gelatinous adhesive with the razor and Kimwipe. Wipe off any residual Xylene without allowing tissue to dry, and store in 2X SSC at 4˚C until staining.
For the H&E staining protocol, continue to the next section. To continue to the Immunofluorescence (IF) staining protocol (Antibody staining), see below.
You will need the following materials and reagents for this step: staining jars, SelecTech Hematoxylin 560 (Leica Biosystems 3801570), SelecTech Defining Solution (Leica Biosystems 3803590), SelecTech Blue Buffer 8 (Leica Biosystems 3802915), SelecTech Alcoholic Eosin Y 515 (Leica Biosystems 3801615), MM24 Mounting Medium (VWR 3801120), Xylene, distilled water (dH2O).
Dilute SelecTech Blue Buffer 8 1:20 in distilled water (dH2O) before use.
Prepare a total of 16 total staining jars for the H&E staining steps:
Due to the hazardous properties of Xylene, the Xylene steps should be done in the hood following your laboratory guidelines. Hematoxylin, post-hematoxylin water, and Alcoholic Eosin Y are considered dye-containing waste and should be disposed of properly. Defining solution contains alcohol and should be disposed of properly. Dispose of all other chemical waste following your laboratory guidelines.
The following steps are done at room temperature unless otherwise noted:
Prior to mounting the coverslip, ensure that the slide is dry. Moisture on the surface of the slide may result in poor mounting.
Wipe away any residual droplets with a Kimwipe being careful not to touch the tissue with the Kimwipe.
Samples may be stored temporarily at 4°C and should be imaged within 3 days after mounting.
Some loss of staining efficiency is expected during the post-run H&E. However, the following steps can be used to improve imbalanced H&E images (Figure 4):
You will need the following materials and reagents for this step: staining jars, 2X SSC, compatible fluorescent labeled antibodies, staining tray with cover.
Samples may be stored temporarily at 4°C covered and protected from light and should be imaged within 3 days.
The following antibodies have been tested by NanoString for post-run IF staining:
NOTE: these antibodies have been tested but not yet validated. The use of any antibody may require empirical testing and optimization. This protocol is optimized for the use of primary conjugated antibodies for post-run IF staining. If the use of a secondary antibody is required, contact [email protected].
Additional antibodies may be used but will require empirical testing. For a list of antibodies and morphology markers tested with NanoString's GeoMx® DSP platform, which should be suitable for use with post-run CosMx SMI tissue, visit https://nanostring.com/products/geomx-digital-spatial-profiler/geomx-morphology-markers/.
Special thanks to the Chun lab at the Cumming School of Medicine, University of Calgary; the Ginhoux lab at the Singapore Immunology Network, Agency for Science, Technology, and Research; and the Parfitt Ophthalmology Discovery Research lab at AbbVie for permission to publish the post-run IF images of their tissue samples run through the NanoString Technology Access Program (Figure 5A, B, and C respectively).
Thank you for choosing CosMx. If you have any further questions or need assistance, please don't hesitate to contact our Support team ([email protected]).