HDMA Raw Data Metadata

This metadata record provides details of the raw data produced from the SHARE-seq experiments for the HDMA study (Liu et al. bioRxiv 2025). Summary De-identified tissue samples were collected at Stanford University School of Medicine from elective termination of pregnancy procedures with informed consent for the research use of tissues in observance of relevant legal and institutional ethical regulations. SHARE-seq was performed on isolated nuclei (Methods, Note S1). In total, N=76 samples were profiled, from across 10-23 post-conception weeks, and covering a total of 12 tissues. The full list of samples, along with experimental batch, age, and sex, is provided in Supplementary Table 1. SHARE-seq library raw data files All DNA libraries were sequenced on a NovaSeq 6000 using 300-cycle S4 v1.5 reagent kits with XP workflow. Paired-end sequencing was run with a 96-99-8-96 configuration (Read1-Index1-Index2-Read2). Sequencing was performed at the Stanford Genome Technology Center. We developed a highly parallelized, rapid, and storage-efficient pre-processing pipeline to convert BCL files from sequencers to ATAC fragment files and RNA sparse matrices (Fig. S1, Methods, and available in full at https://github.com/GreenleafLab/shareseq-pipeline (stable release v1.0.0). The raw data is in the form of anonymized FASTQs pairs per sample per data modality, and have been deposited to SRA (PRJNA1402391). Reads have been anonymized using Bamboozle. SHARE-seq library processed data Processed data in the form of fragments per sample (ATAC modality) and gene expression count matrices (RNA modality) are provided. The full list of datasets deposited is provided in Supplementary Table 14.