This readme.txt file was generated on 2024-09-23 by Recommended citation for the data: De Carvalho Nunes, Allancer Divino. (2024). Attenuation of cellular senescence and improvement of osteogenic differentiation capacity of human liver stem cells using specific senomorphic and senolytic agents. Retrieved from the Data Repository for the University of Minnesota (DRUM),http://doi.org/10.13020/6bja-xt15. ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset: Attenuation of cellular senescence and improvement of osteogenic differentiation capacity of human liver stem cells using specific senomorphic and senolytic agents 2. Author Information Author Contact: Allancer Divino De Carvalho Nunes (anunes@umn.edu) Name: Allancer Divino De Carvalho Nunes Institution:University of Minnesota Email: anunes@umn.edu ORCID:0000-0003-4158-683X 3. Date published or finalized for release: 2024-09-23 4. Date of data collection: January/2023 5. Geographic location of data collection (where was data collected?):Minneapolis, Minnesota, USA 6. Information about funding sources that supported the collection of the data: This work was supported by NIH grants U19 AG056278, P01 AG062413, U54 AG079754, U54 AG076041, R01 AG069819 and RO1 AG063543 to Paul D. Robbins. 7. Overview of the data (abstract): Expansion of adult stem cells in culture increases the percent of senescent cells, reduces their differentiation capacity and limits their clinical use. Senotherapeutics have been demonstrated to attenuate many aging phenotypes by suppressing cellular senescence and improving the functionality of aged cells. Thus, we investigated whether treatment with certain senotherapeutic drugs would reduce the accumulation of senescent cells during expansion of adult human stem cells while maintaining their differentiation capacity, thereby improving their clinical effectiveness. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC0 1.0 Universal (http://creativecommons.org/publicdomain/zero/1.0/) 2. Links to publications that cite or use the data: 3. Was data derived from another source? No If yes, list source(s): 4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/policies/#drum-terms-of-use --------------------- DATA & FILE OVERVIEW --------------------- Filename: HLSCP11CTRL2_S1_R1_001.fastq.gz Short description: Raw fastq file for bulk RNA-seq for the forward sequence of a Control HLSC sample in passage 11. Filename: HLSCP11CTRL2_S1_R2_001.fastq.gz Short description: Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 11. Filename: HLSCP16CTRL2_S13_L002_R2_001.fastq.gz.gz Short description: Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 16. Filename: HLSCP11CTRL5_S10_L002_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 11. Filename: HLSCP11CTRL6_S16_L002_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 11. Filename: HLSCP11CTRL6_S16_L002_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 11. Filename: HLSCP16CTRL2_S13_L002_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 16. Filename: HLSCP11CTRL5_S10_L002_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 11. Filename: HLSCP11XJB1_R1_paired.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a XJB-5-131 HLSC sample in passage 11. Filename: HLSCP6CTRL5_S18_L002_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 6. Filename: HLSCP6CTRL2_S4_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 6. Filename: HLSCP6CTRL5_S18_L002_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 6. Filename: HLSCP6CTRL2_S4_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 6. Filename: HLSCP6CTRL2_S4_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 6. Filename: HLSCP11CTRL3_S2_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 11. Filename: HLSCP11CTRL3_S2_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 11. Filename: HLSCP11CTRL4_S3_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 11. Filename: HLSCP11CTRL4_S3_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 11. Filename: HLSCP11CTRL8_S4_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 11. Filename: HLSCP11CTRL8_S4_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 11. Filename: HLSCP11DQ2_S5_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 11 treated with DQ. Filename: HLSCP11DQ2_S5_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 11 treated with DQ. Filename: HLSCP11DQ3_S6_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 11 treated with DQ. Filename: HLSCP11DQ3_S6_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 11 treated with DQ. Filename: HLSCP11DQ4_S7_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 11 treated with DQ. Filename: HLSCP11DQ4_S7_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 11 treated with DQ. Filename: HLSCP11DQ5_S8_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 11 treated with DQ. Filename: HLSCP11DQ5_S8_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 11 treated with DQ. Filename: HLSCP11XJB2_S6_L002_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 11 treated with XJB-5-131. Filename: HLSCP11XJB2_S6_L002_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 11 treated with XJB-5-131. Filename: HLSCP11XJB5_S12_L002_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 11 treated with XJB-5-131. Filename: HLSCP11XJB5_S12_L002_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 11 treated with XJB-5-131. Filename: HLSCP11XJB6_S17_L002_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 11 treated with XJB-5-131. Filename: HLSCP11XJB6_S17_L002_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 11 treated with XJB-5-131. Filename: HLSCP16CTRL3_S7_L002_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 16. Filename: HLSCP16CTRL3_S7_L002_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 16. Filename: HLSCP16CTRL4_S1_L002_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 16. Filename: HLSCP16CTRL4_S1_L002_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 16. Filename: HLSCP16CTRL8_S12_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 16. Filename: HLSCP16CTRL8_S12_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a Control HLSC sample in passage 16. Filename: HLSCP16DQ1_S13_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 16 treated with DQ. Filename: HLSCP16DQ1_S13_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 16 treated with DQ. Filename: HLSCP16DQ5_S14_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 16 treated with DQ. Filename: HLSCP16DQ5_S14_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 16 treated with DQ. Filename: HLSCP16DQ7_S15_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 16 treated with DQ. Filename: HLSCP16DQ7_S15_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 16 treated with DQ. Filename: HLSCP16DQ8_S16_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 16 treated with DQ. Filename: HLSCP16DQ8_S16_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 16 treated with DQ. Filename: HLSCP16XJB5_S5_L002_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 16 treated with XJB-5-131. Filename: HLSCP16XJB5_S5_L002_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 16 treated with XJB-5-131. Filename: HLSCP16XJB6_S11_L002_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 16 treated with XJB-5-131. Filename: HLSCP16XJB6_S11_L002_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 16 treated with XJB-5-131. Filename: HLSCP16XJB7_S5_R1_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 16 treated with XJB-5-131. Filename: HLSCP16XJB7_S5_R2_001.fastq.gz.gz Short description:Raw fastq file for bulk RNA-seq for the reverse sequence of a HLSC sample in passage 16 treated with XJB-5-131. 2. Relationship between files: All data were extracted from Human Liver Stem Cells (HLSCs) in different passages treated with different senotherapeutics or control. These files are the raw data for the forward and reverse reads for a HLSC Control sample in passage 11 that are utilized together for paired-end read analysis. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Unique dual indexed paired-end TruSeq stranded libraries were created and pooled following rRNA depletion using the Ribo-Zero Plus rRNA Depletion kit. All libraries were gel size selected (≈ 200bp) and sequenced using an Illumina NovaSeq X Lane with a 2 x 150bp flow cell. Libraries were sequenced to a mean depth of ≥20M reads 2. Methods for processing the data: Fastqc files were processed using Trimmomatic for the removal of adapter sequences and bases having a Q-score < 30. The quality of trimmed fastqc files were confirmed using FastQC. Paired-end reads were aligned to the GRCh38 reference genome using Hisat2 v2.0.5 and feature Counts v1.5.0 was used count and map each gene 3. Instrument- or software-specific information needed to interpret the data:Pre-filtering removing low count reads (≤5) and Differential Gene expression (DEG) analysis was done in R v4.4.0 using the package DESeq2 v3.19 and a false discovery rate cut off of 0.05. 4. Standards and calibration information, if appropriate: None. 5. Environmental/experimental conditions: For Analysis in R (script is not included): > sessionInfo() R version 4.4.0 (2024-04-24) Platform: x86_64-pc-linux-gnu Running under: Rocky Linux 8.10 (Green Obsidian) Matrix products: default BLAS/LAPACK: /common/software/install/manual/openblas/0.3.27_gcc11.3.0/lib/libopenblasp-r0.3.27.so; LAPACK version 3.12.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C time zone: America/Chicago tzcode source: system (glibc) attached base packages: [1] grid parallel stats4 stats graphics grDevices utils [8] datasets methods base other attached packages: [1] RNAAgeCalc_1.16.0 msigdbr_7.5.1 [3] org.Mm.eg.db_3.19.1 VennDiagram_1.7.3 [5] futile.logger_1.4.3 gridExtra_2.3 [7] enrichplot_1.24.4 magrittr_2.0.3 [9] biomaRt_2.60.1 ape_5.8 [11] clustree_0.5.1 ggraph_2.2.1 [13] SingleR_2.6.0 celldex_1.14.0 [15] GenomicFeatures_1.56.0 org.Hs.eg.db_3.19.1 [17] AnnotationDbi_1.66.0 DOSE_3.30.5 [19] ReactomePA_1.48.0 ggsignif_0.6.4 [21] ggpubr_0.6.0.999 tiff_0.1-12 [23] Matrix_1.7-1 pheatmap_1.0.12 [25] clusterProfiler_4.12.6 Seurat_5.2.0 [27] SeuratObject_5.0.2 sp_2.1-4 [29] airway_1.24.0 lubridate_1.9.4 [31] forcats_1.0.0 stringr_1.5.1 [33] dplyr_1.1.4 purrr_1.0.2 [35] readr_2.1.5 tidyr_1.3.1 [37] tibble_3.2.1 ggplot2_3.5.1 [39] tidyverse_2.0.0 DESeq2_1.44.0 [41] SummarizedExperiment_1.34.0 Biobase_2.64.0 [43] MatrixGenerics_1.16.0 matrixStats_1.4.1 [45] GenomicRanges_1.56.2 GenomeInfoDb_1.40.1 [47] IRanges_2.38.1 S4Vectors_0.42.1 [49] BiocGenerics_0.50.0 loaded via a namespace (and not attached): [1] R.methodsS3_1.8.2 progress_1.2.3 [3] nnet_7.3-19 goftest_1.2-3 [5] Biostrings_2.72.1 HDF5Array_1.32.1 [7] vctrs_0.6.5 spatstat.random_3.3-2 [9] digest_0.6.37 png_0.1-8 [11] gypsum_1.0.1 ggrepel_0.9.6 [13] deldir_2.0-4 parallelly_1.41.0 [15] MASS_7.3-60.2 reshape2_1.4.4 [17] foreach_1.5.2 bumphunter_1.46.0 [19] httpuv_1.6.15 qvalue_2.36.0 [21] withr_3.0.2 xfun_0.50 [23] ggfun_0.1.8 doRNG_1.8.6.1 [25] survival_3.5-8 memoise_2.0.1 [27] gson_0.1.0 tidytree_0.4.6 [29] zoo_1.8-12 pbapply_1.7-2 [31] R.oo_1.27.0 prettyunits_1.2.0 [33] Formula_1.2-5 derfinder_1.38.0 [35] KEGGREST_1.44.1 promises_1.3.2 [37] httr_1.4.7 downloader_0.4 [39] rstatix_0.7.2 restfulr_0.0.15 [41] globals_0.16.3 fitdistrplus_1.2-2 [43] rhdf5filters_1.16.0 rstudioapi_0.17.1 [45] rhdf5_2.48.0 UCSC.utils_1.0.0 [47] miniUI_0.1.1.1 generics_0.1.3 [49] base64enc_0.1-3 reactome.db_1.88.0 [51] babelgene_22.9 curl_6.1.0 [53] zlibbioc_1.50.0 ScaledMatrix_1.12.0 [55] polyclip_1.10-7 GenomeInfoDbData_1.2.12 [57] ExperimentHub_2.12.0 SparseArray_1.4.8 [59] xtable_1.8-4 evaluate_1.0.3 [61] S4Arrays_1.4.1 BiocFileCache_2.12.0 [63] hms_1.1.3 irlba_2.3.5.1 [65] colorspace_2.1-1 filelock_1.0.3 [67] ROCR_1.0-11 reticulate_1.40.0 [69] spatstat.data_3.1-4 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spatstat.univar_3.1-1 [179] R.utils_2.12.3 lazyeval_0.2.2 [181] alabaster.base_1.4.2 shiny_1.10.0 [183] htmltools_0.5.8.1 GO.db_3.19.1 [185] sctransform_0.4.1 formatR_1.14 [187] rappdirs_0.3.3 glue_1.8.0 [189] spam_2.11-0 httr2_1.0.7 [191] XVector_0.44.0 RCurl_1.98-1.16 [193] treeio_1.28.0 BSgenome_1.72.0 [195] recount_1.30.2 igraph_2.1.2 [197] R6_2.5.1 rngtools_1.5.2 [199] cluster_2.1.6 Rhdf5lib_1.26.0 [201] aplot_0.2.4 DelayedArray_0.30.1 [203] tidyselect_1.2.1 htmlTable_2.4.3 [205] xml2_1.3.6 ggforce_0.4.2 [207] car_3.1-3 future_1.34.0 [209] rsvd_1.0.5 munsell_0.5.1 [211] KernSmooth_2.23-22 data.table_1.16.4 [213] htmlwidgets_1.6.4 fgsea_1.30.0 [215] RColorBrewer_1.1-3 rlang_1.1.4 [217] spatstat.sparse_3.1-0 spatstat.explore_3.3-3 [219] rentrez_1.2.3 6. Describe any quality-assurance procedures performed on the data: RNA submitted for sequencing under went QC via nano drop and Bioanalyzer prior to library construction and sequencing where other quality control assays were conducted by the university of Minnesota Genomics core following 10X genomics SOP for paired-end RNA sequencing. Following sequencing, all adapter sequences were removed, all reads contained base q-scores of >30 and only high quality paired reads were used for downstream analysis excluding genes that had a total count of <5 in the dataset. 7. People involved with sample collection, processing, analysis and/or submission: Allancer Nunes and Louise E Pitcher