Spatial Transcriptomics of Human Fetal Lungs

Spatial transcriptomic profiles were generated using lung tissue sections obtained from twelve prenatal human lung samples ranging in gestational age from 13 – 20 weeks, of which four were diagnosed with Trisomy 21, with defined hypoplasia. Overall design: Lung tissue sections were assessed for quality using DV200 criteria, and those with DV200 values greater than 50% were selected for spatial transcriptomics. 5-micron tissue sections from individual samples were placed onto Visium Gene Expression Slides (10X Genomics), stained with H&E using Visium chemistry (v1) and scanned, in two batches. Subsequently, the tissue samples were permeabilized to release ligated probe pairs from the cells, that are bound to the spatially barcoded oligonucleotides present on the spots. The resulting barcoded libraries were sequenced on a NovaSeq 6000 sequencer (Illumina) and aligned to GRCh38-2020-A and quantified using the standard Spaceranger workflow (v2.0.1).