/Urine-single-cell-sequencing-AKI

This repository contains code and data from the publication "Urinary single-cell sequencing captures intrarenal injury and repair processes in human acute kidney injury", currently uploaded as a preprint to biorxiv: https://doi.org/10.1101/2022.02.15.479234

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Urine-single-cell-sequencing-AKI

This repository contains code and data from the publication "Urinary single-cell sequencing captures intrarenal injury and repair processes in human acute kidney injury", currently uploaded as a preprint to biorxiv: https://doi.org/10.1101/2022.02.15.479234

You'll find several scripts containing the code for analysis and plotting found in the manuscript:

  1. "AKI_Urine_Sediment_SO_script" contains the code for generating the whole data Seurat object ("SO_all_urine_cells.rds"/"URINE") and subsetted renal cell Seurat object ("SO_all_kidney_cells.rds"/"RENAL") from raw data
  2. "AKI_Urine_Sediment_Demultiplexing_pooled_samples_script" contains the code used to demultiplex barcoded and pooled urine samples as well as the code for Suppl.Fig. 3
  3. "AKI_Urine_Sediment_Figure1_script" contains the code for Fig. 1 and Suppl. Fig. 4-5
  4. "AKI_Urine_Sediment_Figure2_script" contains the code for Fig. 2 and Suppl. Fig. 6-8, 17
  5. "AKI_Urine_Sediment_Figure3_script" contains the code for Fig. 3 and Suppl. Fig. 9, 10, 13
  6. "AKI_Urine_Sediment_Figure4_script" contains the code for Fig. 4
  7. "AKI_Urine_Sediment_Figure5_script" contains the code for Fig. 5 and Suppl. Fig. 11-12
  8. "AKI_Urine_Sediment_Figure6_script" contains the code for Fig. 6 and Suppl. Fig. 14
  9. "AKI_Urine_Sediment_SupplFig15_script" contains the code for Suppl. Fig. 15
  10. "AKI_Urine_Sediment_SupplFig16-20_script" contains the code for Suppl. Fig. 16, 18-20
  11. "AKI_Urine_Sediment_SupplFig21_script" contains the code for Suppl. Fig. 21

Some additional data is provided in form of these documents:

DEG_all_urine_cells.rds = Table with differentially expressed genes from SO_all_urine_cells.rds
DEG_kidney_urine_cells.rds = Table with differentially expressed genes from SO_kidney_urine_cells.rds

Urine_AKI_patient_data.csv = patient information added as metadata in "AKI_Urine_Sediment_SO_script" Urine_AKI_barcode_list.csv = barcode patient information used in "AKI_Urine_Sediment_Demultiplexing_pooled_samples_script" Urine_AKI_urine_output_crea_data.csv = longitudinal info on serum creatinine and urine output for patients sampled multiple times (fig. 6) Urine_AKI_post_QC_cellnames.rds = list of cells comprising the whole data Seurat object ("SO_all_urine_cells.rds"/"URINE") post quality control

The raw data will be uploaded to the NCBI GEO repository and linked here upon peer-reviewed publication.