Decoding myofibroblast origins in human kidney fibrosis
Zenodo (CERN European Organization for Nuclear Research)
Abstract
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 (rkramann@ukaachen.de) 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)
Authors 29
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Christoph Kuppe Aachen
Affiliation as printed
RWTH Aachen
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Mahmoud M. Ibrahim Aachen
Affiliation as printed
RWTH Aachen
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Sankt-Antonius-Hospital Eschweiler
Affiliation as printed
St. Antonius Hospital Eschweiler
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Xiaoting Zhang Aachen
Affiliation as printed
RWTH Aachen
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Susanne Maria Ziegler Aachen
Affiliation as printed
RWTH Aachen
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Jitske Jansen Aachen
Affiliation as printed
RWTH Aachen
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Katharina C. Reimer Aachen
Affiliation as printed
RWTH Aachen
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Affiliation as printed
Heidelberg University
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Affiliation as printed
University of Edinburgh
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Affiliation as printed
University of Edinburgh
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Affiliation as printed
University of Edinburgh
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Maurice Halder Aachen
Affiliation as printed
RWTH Aachen
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Yaoxian Xu Aachen
Affiliation as printed
RWTH Aachen
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Nazanin Kabgani Aachen
Affiliation as printed
RWTH Aachen
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Nadine Kaesler Aachen
Affiliation as printed
RWTH Aachen
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University Medical Center Hamburg-Eppendorf
Affiliation as printed
University Medical Center Hamburg-Eppendorf
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University Medical Center Hamburg-Eppendorf
Affiliation as printed
University Medical Center Hamburg-Eppendorf
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University Medical Center Hamburg-Eppendorf
Affiliation as printed
University Medical Center Hamburg-Eppendorf
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University Medical Center Hamburg-Eppendorf
Affiliation as printed
University Medical Center Hamburg-Eppendorf
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Peter Boor Aachen
Affiliation as printed
RWTH Aachen
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Sylvia Menzel Aachen
Affiliation as printed
RWTH Aachen
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Affiliation as printed
Erasmus Medical Center Rotterdam
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Affiliation as printed
Erasmus Medical Center Rotterdam
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Sankt-Antonius-Hospital Eschweiler
Affiliation as printed
St. Antonius Hospital Eschweiler
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Floege Jürgen Aachen
Affiliation as printed
RWTH Aachen
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Rebekka K. Schneider Aachen
Affiliation as printed
RWTH Aachen
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Affiliation as printed
University of Heidelberg
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Affiliation as printed
University of Edinburgh
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Rafael Kramann Aachen
Affiliation as printed
RWTH Aachen
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