A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease

Description

Data availability

All sequencing data were analyzed using the GRCh38 (hg38) reference genome. For published data from the KPMP/HuBMAP atlas, access to the raw snRNAseq data has been detailed in the Lake et al manuscript (Nature 2023, in press, https://doi.org/10.1038/s41586-023-05769-3). These raw sequencing data are under controlled access (human data) as they are potentially identifiable and can be accessed from the following respective sources: 1) KPMP data has been deposited at https://atlas.kpmp.org/repository/ and can be requested and made available by signing a data use agreement (DUA) with KPMP. KPMP will respond to initial data requests within 12–36 h and provide data up to one month after DUA has been signed. Manuscripts resulting from KPMP controlled access data are requested to go through the KPMP Publications and Presentations Committee which reviews and approves manuscripts every two weeks. Any analysis resulting from KPMP data may be published or shared so long as it does not re-identify KPMP participants. 2) The HuBMAP raw data are available for download from the database of Genotypes and Phenotypes (dbGaP, phs002249) by requesting for authorized access following instructions on the dbGaP website. The process to request access to this dbGaP study is here: https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?adddataset=phs002249&page=login. Briefly, to download the human sequence data for this study after obtaining authorization from the NIH Data Access Committee, one would go through the Sequence Read Archive here: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA671343. Processed data (published in the Lake et al manuscript) for both of these sources is available in the GEO Super-series: GSE183279 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE183279). The new snRNAseq data generated for this study (raw sequencing and processed), along with all the Visium spatial transcriptomic data are available in GEO as the Super-series GSE231630 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE231630 or deposited in the HuBMAP portal (https://portal.hubmapconsortium.org/). A breakdown of the data availability of all papillary samples is presented in Supplementary Table 2. Source data are provided with this paper. For the imaging data: the source data for all the main and supplementary figures (3D imaging, CODEX, and smFISH) are available at the following repository: https://doi.org/10.5281/zenodo.7653239 and https://zenodo.org/record/7653239#.ZGIuGc7MKUk Source data are provided with this paper.

The R packages and code used in the snRNAseq and spatial transcriptomics analysis are described in the methods. For image analysis, the VTEA software is available for download through the FIJI plugin updater with the source code is available on GitHub, https://github.com/icbm-iupui/volumetric-tissue-exploration-analysis. Additional descriptions and vignettes demonstrating the use of VTEA are available at https://vtea.wiki.