title: GSM8995843: NTM-infected mouse lung tissue – Atg7 WT (control), spatial transcriptomics; Mus musculus; OTHER
library_name: GSM8995843
library_construction_protocol: Tissue samples were processed using Visium CytAssist Spatial Gene Expression for FFPE protocol. Lung tissues from Mav-infected Atg7 cWT and Atg7 cKO mice (21 dpi) were fixed in 10% neutral buffered formalin, embedded in paraffin, and sectioned at 5 µm thickness using a microtome. Sections were placed on Visium CytAssist slides and processed following the manufacturer's protocol (10x Genomics #CG000409). RNA was extracted using the RNeasy FFPE Kit (Qiagen #73504) after deparaffinization (Qiagen Deparaffinization Solution #19093). RNA integrity was assessed using Agilent TapeStation (High Sensitivity RNA ScreenTape #5067-5579) by measuring DV200 values. Libraries were prepared from FFPE tissue sections using the Visium Spatial Gene Expression for FFPE Kit, Mouse Transcriptome v1 (10x Genomics #1000521) and Dual Index Kit TS Set A (10x Genomics #1000251) following the manufacturer's instructions. H&E staining was performed prior to permeabilization using standard reagents (Xylene, Ethanol, Eosin Y, Mayer's Hematoxylin, Bluing Reagent), and imaging was conducted using Nikon Eclipse Ti2 microscope (QC at 4X, Visium at 20X).