Dataset Open Access

Decoding myofibroblast origins in human kidney fibrosis

Kuppe, Christoph; Ibrahim, Mahmoud M; Kranz, Jennifer; Zhang, Xiaoting; Ziegler, Susanne; Jansen, Jitske; Reimer, Katharina C; Perales-Paton, Javier; Smith, James R; Dobie, Ross; Wilson-Kanamari, John R; Halder, Maurice; Xu, Yaoxian; Kabgani, Nazanin; Kaesler, Nadine; Klaus, Martin; Gemhold, Lukas; Puelles, Victor G; Huber, Tobias B; Boor, Peter; Menzel, Sylvia; Hoogenboezem, Remco M; Bindels, Eric M J; Steffens, Joachim; Jürgen, Floege; Schneider, Rebekka K; Saez-Rodriguez, Julio; Henderson, Neil C; Kramann, Rafael

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)

 

Files (2.1 GB)
Name Size
github_files.tar.gz
md5:1ae202b7fa5e157e55d95118ad1ddb59
562.8 MB Download
Human_CD10negative.tar.gz
md5:4af0d2909c2fb1053f3e772eaebedefe
257.1 MB Download
Human_CD10plus.tar.gz
md5:d002584a13ff52ddd5664ac69aab8243
108.5 MB Download
Human_PDGFRb.tar.gz
md5:40db3d3d4c053034b33608d0a28f977d
242.9 MB Download
Human_PDGFRBplus_TFanalysis.tar.gz
md5:be1b77e0ffa6d6df97a2227f61c4f29e
328.1 kB Download
HumanPDGFRBpositive_Nkd2_grnboost2.csv
md5:ac2732a529787a8a69323745cde2ba2e
1.2 MB Download
invitro_bulk_rnaseq.tar.gz
md5:81846447a68defcc15638b1970c3ac8b
79.3 MB Download
Mouse_PDGFRab.tar.gz
md5:e08df97a4a5b2d9cd103e1ebc298f99d
71.0 MB Download
Mouse_PDGFRb.tar.gz
md5:fdfaaac203e49a63cbdf83fa58355fda
20.4 MB Download
mouse_uuo_pdgfrab_atacseq.bw
md5:a2336e505a99de8828d337f0b7f9b4cd
713.1 MB Download
mouse_uuo_pdgfrab_motifs.meme
md5:d82c72845acbd9a7000f87029d4f4517
16.7 kB Download
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