Decoding myofibroblast origins in human kidney fibrosis

<p>Data repository for the manuscript: Kuppe, Ibrahim et al. &quot;Decoding myofibroblast origins in human kidney fibrosis&quot;, 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.</p> <p>For further data requests and questions, please contact Dr. Rafael Kramann (rkramann@ukaachen.de)</p> <p>&nbsp;</p> <p>File Details:</p> <p>- Human in vitro PDGFRb+ RNA-seq (bulk RNA-seq data for various NKD2 knock-out and knock-in clones)<br> * invitro_bulk_rnaseq.tar.gz: Salmon output for all samples. Please see the manuscript for further information.</p> <p>- UUO Mouse FACS sorted PDGFRa+/b+ ATAC-Seq<br> * 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)<br> * mouse_uuo_pdgfrab_motifs.meme: Motifs identified based on the ATAC-Seq data and further analyzed in the paper</p> <p>- UUO and Sham Mouse FACS sorted PDGFRa+/b+ scRNA-seq (10x Genomics)<br> * 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.</p> <p>- UUO and Sham Mouse FACS sorted PDGFRb+ scRNA-seq (SmartSeq2)<br> * 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.</p> <p>- Human FACS sorted CD10+ scRNA-seq (10x Genomics)<br> * 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.</p> <p>- Human FACS sorted CD10- scRNA-seq (10x Genomics)<br> * 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.</p> <p>- Human FACS sorted PDGFRb+ scRNA-seq (10x Genomics)<br> * 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.<br> * HumanPDGFRBpositive_Nkd2_grnboost2.csv: Gene Regulatory Network obtained by GRNboost2 on genes correlated with NKD2 in Fibroblast (Mesenchymal) cells. See manuscript for details.<br> * Human_PDGFRBplus_TFanalysis.tar.gz: TF analysis based on single cell RNA-seq for promoter and distal regions. See manuscript for details.</p> <p>&nbsp;</p> <p>&nbsp;</p> <p>- github_files.tar.gz: RData Objects associated with the paper code repository (https://github.com/mahmoudibrahim/KidneyMap)</p> <p>&nbsp;</p>