CODEX of mouse tumor draining lymph nodes

ABSTRACT: Freshly obtained PPM TDLN and tumor samples were frozen and embedded in OCT (Sakura Finetek Usa) via a bath of isopentane (Millipore Sigma) and liquid nitrogen, and 6 µm thick sections of frozen blocks were acquired and mounted to coverslips (Electron Microscopy Science) coated with poly-l-lysine (Sigma Aldrich). CODEX samples were prepared as previously described and stained with antibody-DNA barcode conjugations. CODEX sample imaging was done by connecting a CODEX robot (Akoya Biosciences) to a Zeiss Axio Observer 7 microscope (Carl Zeiss microscopy) that was equipped with a Calibri 7 light source (405, 493, 575, 654, 761 nm excitations) and Prime BSI camera (Photometrics). A Plan-Apochromat 20x/0.8 NA M27 objective was used to collect 16-bit four-channel images and a 10 ms exposure time for DAPI, 300 ms for ATTO550, AF647 and AF750. 112 HE DAPI/GFP/Cy3/Cy5/Cy7 filter was used for all channels and definite focus was used to keep samples focused during the imaging process. 200-500 tiles were collected for each sample depending on the sample size.

ORGANISM(S): Mus musculus

SUBMITTER: Han Dong 

PROVIDER: S-BSST2926 | biostudies-other |

SECONDARY ACCESSION(S): 10.1038/s41590-026-02512-8

REPOSITORIES: biostudies-other