Decoding myofibroblast origins in human kidney fibrosis

Data repository for the manuscript: Kuppe, Ibrahim et al. "Decoding myofibroblast origins in human kidney fibrosis", 2020. Please also consult the supplemental data in the paper, and the data availability statement in hte manuscript for raw FASTQ files for mouse data. For further data requests and questions, please contact Dr. Rafael Kramann ([email protected]) File Details: - Human in vitro PDGFRb+ RNA-seq (bulk RNA-seq data for various NKD2 knock-out and knock-in clones) * invitro_bulk_rnaseq.tar.gz: Salmon output for all samples. Please see the manuscript for further information. - UUO Mouse FACS sorted PDGFRa+/b+ ATAC-Seq * mouse_uuo_pdgfrab_atacseq.bw: BigWig Signal file for ATAC-Seq data, PDGFRa+/b+ FACS sorted cells from day 10 UUO mouse kidneys (average of two biological replicates) * mouse_uuo_pdgfrab_motifs.meme: Motifs identified based on the ATAC-Seq data and further analyzed in the paper - UUO and Sham Mouse FACS sorted PDGFRa+/b+ scRNA-seq (10x Genomics) * Mouse_PDGFRab.tar.gz: contains the count data derived by Alevin/Salmon for the cells analyzed in the paper in matrix market format (.mtx). column data include cell cluster annotations. - UUO and Sham Mouse FACS sorted PDGFRb+ scRNA-seq (SmartSeq2) * Mouse_PDGFRa.tar.gz: contains the expression data for the cells analyzed in the paper in matrix market format (.mtx). column data include cell cluster annotations. - Human FACS sorted CD10+ scRNA-seq (10x Genomics) * Human_CD10plus.tar.gz: contains the count data derived by Alevin/Salmon for the cells analyzed in the paper in matrix market format (.mtx). column data include cell cluster annotations. - Human FACS sorted CD10- scRNA-seq (10x Genomics) * Human_CD10minus.tar.gz: contains the count data derived by Alevin/Salmon for the cells analyzed in the paper in matrix market format (.mtx). column data include cell cluster annotations. - Human FACS sorted PDGFRb+ scRNA-seq (10x Genomics) * Human_PDGFRb.tar.gz: contains the count data derived by Alevin/Salmon for the cells analyzed in the paper in matrix market format (.mtx). column data include cell cluster annotations. * HumanPDGFRBpositive_Nkd2_grnboost2.csv: Gene Regulatory Network obtained by GRNboost2 on genes correlated with NKD2 in Fibroblast (Mesenchymal) cells. See manuscript for details. * Human_PDGFRBplus_TFanalysis.tar.gz: TF analysis based on single cell RNA-seq for promoter and distal regions. See manuscript for details. - github_files.tar.gz: RData Objects associated with the paper code repository (https://github.com/mahmoudibrahim/KidneyMap)

Kuppe, C., Ibrahim, M. M., Kranz, J., Zhang, X., Ziegler, S., Jansen, J., Reimer, K. C., Perales-Paton, J., Smith, J. R., Dobie, R., Wilson-Kanamari, J. R., Halder, M., Xu, Y., Kabgani, N., Kaesler, N., Klaus, M., Gemhold, L., Puelles, V. G., Huber, T. B., … Kramann, R. (2020). Decoding myofibroblast origins in human kidney fibrosis (Version 1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.4059315