title: GSM9040243: E2-I1E-C-IBA1-007; Mus musculus; OTHER
library_construction_protocol: FFPE kidney sections were deparaffinized, rehydrated, and subjected to antigen retrieval in Tris-EDTA buffer (pH 9.0) followed by proteinase K digestion. Mouse Whole Transcriptome Atlas probes were hybridized to the tissue at 37°C for 16–24 hours. After washing, UV-cleavable oligonucleotide tags were released from selected regions of interest (ROIs) and collected into a 96-well plate for library preparation. FFPE kidney sections were processed using the NanoString GeoMx DSP with the Mouse Whole Transcriptome Atlas. After deparaffinization, antigen retrieval, and proteinase K digestion, probes were hybridized overnight. Slides were stained with SYTO 13, PanCK-AF532, CD10-AF647, and IBA1-AF594 to guide ROI selection in cortex and medulla. UV-cleaved oligonucleotide tags from selected AOIs were collected into a 96-well plate and amplified using Illumina i5/i7 dual indexing primers. Libraries were purified with AMPure XP beads, quantified by Qubit, quality-checked with Bioanalyzer, and sequenced on an Illumina NextSeq 2000. Data were processed with the GeoMx NGS Pipeline (v1.1).