title: GSM9345031: DORSAL_D16; Mus musculus; RNA-Seq
library_construction_protocol: Organoids were dissociated using the Worthington Papain Dissociation System (#LK003150) following manufacturer instructions. Libraries were prepared using the PIPseq T2 Single Cell RNA v4.0PLUS platform (Fluent #FBSSCRT28V4.05) or Illumina Single Cell 3' RNA Prep, T2 (Illumina #20135689), pooling 3,333 cells per genotype (10,000 total per library). Sequencing was conducted on an AVITI PE75 Flowcell (Element Biosciences) at the UC Davis Technologies Core, generating approximately 900 million reads. Raw FASTQ files were processed using the PIPseeker pipeline (v3.3), with default parameters for alignment, transcript quantification, and cell calling against the GRCm39 mouse reference genome (GENCODE vM29 2022.04, Ensembl 106).