Count tables & seurat objects related to "Single-cell transcriptomics provides insights into hypertrophic cardiomyopathy"
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#### Description The data in this repository contains processed files related to the paper "Single-cell transcriptomics provides insights into hypertrophic cardiomyopathy" by Wehrens et al. (2022), Cell Reports (https://doi.org/10.1016/j.celrep.2022.110809). These files should allow you to reproduce analyses and figures from the paper, without re-mapping the data from FASTQ files (FASTQ files are deposited in the GEO database, under IDs mentioned below -- note that the count tables deposited there are older versions that were not used in the paper). #### Count tables Van Rooij The file `counttables-ROOIJ.zip` contains the following files: | GEO | Patient | Plate | Filename | |-----|---------|--------|----------| | GSM4103885 | Patient 1 | Plate 1 | rJE1_AHFL7NBGX5_S3_cat_pT.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM4103886 | Patient 1 | Plate 2 | JE2_AHY3WGBGX3_S1_cat_pT.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM4103887 | Patient 1 | Plate 3 | JE3_AHY3WGBGX3_S2_cat_pT.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM4103888 | Patient 1 | Plate 4 | JE4_AHFL7NBGX5_S4_cat_pT.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM4103889 | Patient 2 | Plate 1 | JE5_AHFL77BGX5_S6_cat_pT.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM4103890 | Patient 2 | Plate 2 | JE6_AHFL77BGX5_S7_cat_pT.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM4103891 | Patient 2 | Plate 3 | JE7_AHFL7NBGX5_S16_cat_pT.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM4103892 | Patient 2 | Plate 4 | JE8_AHFL7NBGX5_S17_cat_pT.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM4103893 | Patient 3 | Plate 1 | HUB-MW-005_AH32W2BGX9_S5_cat_pT.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM4103894 | Patient 3 | Plate 2 | HUB-MW-006_AH32W2BGX9_S6_cat_pT.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM4103895 | Patient 3 | Plate 3 | HUB-MW-007_HC3GFBGX9_S6_cat_pT.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM4103896 | Patient 3 | Plate 4 | HUB-MW-008_HC3GFBGX9_S7_cat_pT.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM4103897 | Patient 4 | Plate 1 | HUB-JE-010_HGVN3BGX9_S1_cat_pT.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM4103898 | Patient 4 | Plate 2 | HUB-JE-011_HGVN3BGX9_S2_cat_pT.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM4762107 | Patient 5 | Plate 1 | HUB-AL-s001_HG25TBGXF_S5_cat_pT.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM4762108 | Patient 5 | Plate 2 | HUB-AL-s002_HG25TBGXF_S6_cat_pT.nonRibo_E99_Aligned.out.counts.table.tsv | |-----|-------|----------|----------| #### FACS index data The file `FACS_INDEX_data.zip` contains additional recorded data from FACS sorting, related to single cell sizes. Specifically, the file `FSCA__indexData_MW.Rdata` in this archive contains an R object, which contains FACS information (such as FSC_A, FSC_W, FSC_H, SSC_A, SSC_W, SSC_H), and an entry `Cell_newname`, which relates the observations to cellnames in the Seurat objects. - Additional files, where filenames start with a prefix indicating the GEO id: - GSM4103897_indexdata_patient4-plate1__2018-244_exp_cardiologie_plate2.csv - GSM4103898_indexdata_patient4-plate2__2018-244_exp_cardiologie_plate3merged.csv - GSM4762107_indexdata_patient5-plate1_AL1.csv - GSM4762108_indexdata_patient5-plate2_AL2.csv #### Count tables Hu et al. The file `counttables-HU.zip` contains the following files: |-------------|--------------------------------------------------------------------------| | GEO id | Filename | |-------------|--------------------------------------------------------------------------| | GSM2970361 | p.N1.plate.97474.part.1_cat_nc.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM2970361 | p.N1.plate.97474.part.2_cat_nc.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM2970358 | p.N2.plate.97452.part.1_cat_nc.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM2970358 | p.N2.plate.97452.part.2_cat_nc.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM2970358 | p.N2.plate.97493.part.1_cat_nc.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM2970358 | p.N2.plate.97493.part.2_cat_nc.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM2970362 | p.N3.plate.97438.part.1_cat_nc.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM2970362 | p.N3.plate.97438.part.2_cat_nc.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM2970366 | p.N4.plate.97461.part.1_cat_nc.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM2970366 | p.N4.plate.97461.part.2_cat_nc.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM2970360 | p.N5.plate.97458.part.1_cat_nc.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM2970360 | p.N5.plate.97458.part.2_cat_nc.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM3449619 | p.N13.plate.100355.part.1_cat_nc.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM3449619 | p.N13.plate.100355.part.2_cat_nc.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM3449620 | p.N14.plate.104720.part.1_cat_nc.nonRibo_E99_Aligned.out.counts.table.tsv | | GSM3449620 | p.N14.plate.104720.part.2_cat_nc.nonRibo_E99_Aligned.out.counts.table.tsv | |-------------|--------------------------------------------------------------------------| This is data from Wang et al (re-calculated count tables determined by Wehrens et al. paper from selected data as described in the Wehrens et al. methods section). #### Seurat object (Van Rooij only) The file: `H5_RHL_SeuratObject_nM_sel_ROOIJonly.sp.bt_RID2l_clExtended.Rds` contains a Seurat object with only the processed data from Wehrens et al samples: ``` GSM4103885, GSM4103886, GSM4103887, GSM4103888, GSM4103889, GSM4103890, GSM4103891, GSM4103892, GSM4103893, GSM4103894, GSM4103895, GSM4103896, GSM4103897, GSM4103898, GSM4762107, GSM4762108. ``` This Seurat object was used to generate the figures in the paper. #### Seurat object (all) The file `H5_RHL_SeuratObject_nM_sel_ALL.SP_btypSel_RID2l_clExtended.Rds` contains data processed using Seurat as described in Wehrens et al., Wang et al., and Litvinukova et al. Data processing is described in the methods section. This file contains data from: ``` GSM4103885, GSM4103886, GSM4103887, GSM4103888, GSM4103889, GSM4103890, GSM4103891, GSM4103892, GSM4103893, GSM4103894, GSM4103895, GSM4103896, GSM4103897, GSM4103898, GSM4762107, GSM4762108. GSM2970361, GSM2970361, GSM2970358, GSM2970358, GSM2970358, GSM2970358, GSM2970362, GSM2970362, GSM2970366, GSM2970366, GSM2970360, GSM2970360, GSM3449619, GSM3449619, GSM3449620, GSM3449620 ERP123138 ``` This Seurat object was used to generate the figures in the paper.
