GINS_NCB2023

Author: Xiaofeng Huang^1,2,4, Qiao Zhou^1,3,4

¹ Division of Regenerative Medicine & Hartman Institute for Organ Regeneration, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA

² E-mail: xih4001@med.cornell.edu

³ E-mail: jqz4001@med.cornell.edu

⁴ Corresponding

Introduction

The repo contains all codes for analysis in the paper.

Publication associated with this repo

Stomach-derived human insulin-secreting organoids restore glucose homeostasis, Nature Cell Biology, 2023.

Scripts

NOTE: Run Script 1 first to load all the required libraries, helper scripts and colors.

• Script 01: libraries loading; scripts loading; directories; colors
• Script 02: data processing for GINS organoids
• Script 03: data processing for islet
• Script 04: integrating GINS organoids and human islets.
• Script 05: data processing for GINS differentiation time course
• Script 06: comparing hGSC and GINS organoids
• Script 07: comparing hGSC, GINS organoids, and islets
• Script 08: comparing antral and corpus GINS organoids
• Script 09: data processing for GINS graft
• Script 10: comparison GINS organoids, GINS grafts and human islets
• Script 11: visualization of GINS differentiation trajectory
• Script 12: visualization of GINS differentiation trajectory with islet datasets
• Script 13: Regulon analysis
• Script 13: Velocity analysis (Linux)

Figures output

• Script 04: Fig. 3a-c; Extended Data Fig. 4c, 6a
• Script 06: Extended Data Fig. 4a-b, 4e
• Script 07: Fig. 3d; Extended Data Fig. 4d
• Script 08: Extended Data Fig 5d-e
• Script 10: Fig. 4f-g, 6g;
• Script 11: Fig. 5c, 6a; Extended Data Fig 9a-c
• Script 12: Fig. 5a-b,5d-f; Extended Data Fig 8a-c

Data output (no graph plotting)

• Script 4: Extended Data Fig. 6b (pathway enrichment)
• Script 7: Fig. 3d (Signature gene sets)
• Script 12: Fig. 5f (pathway enrichment)

SessionInfo

R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

attached base packages: [1] splines stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] monocle_2.24.0 testthat_3.1.4 DDRTree_0.1.5
[4] irlba_2.3.5 VGAM_1.1-7 Matrix_1.5-1
[7] SCENIC_1.3.1 GENIE3_1.18.0 AUCell_1.18.1
[10] RcisTarget_1.16.0 pheatmap_1.0.12 viridis_0.6.2
[13] viridisLite_0.4.1 patchwork_1.1.2 cowplot_1.1.1
[16] SeuratWrappers_0.3.0 RColorBrewer_1.1-3 DOSE_3.22.0
[19] enrichplot_1.16.1 annotables_0.1.91 org.Hs.eg.db_3.15.0
[22] AnnotationDbi_1.58.0 clusterProfiler_4.4.4 msigdbr_7.5.1
[25] EnhancedVolcano_1.14.0 ggrepel_0.9.1 monocle3_1.2.9
[28] SingleCellExperiment_1.18.0 DoubletFinder_2.0.3 SoupX_1.6.1
[31] SingleR_1.10.0 SummarizedExperiment_1.26.1 Biobase_2.56.0
[34] GenomicRanges_1.48.0 GenomeInfoDb_1.32.3 IRanges_2.30.1
[37] S4Vectors_0.34.0 BiocGenerics_0.42.0 MatrixGenerics_1.8.1
[40] matrixStats_0.62.0 sp_1.5-0 SeuratObject_4.1.0
[43] Seurat_4.1.1 forcats_0.5.2 stringr_1.4.1
[46] dplyr_1.0.9 purrr_0.3.4 readr_2.1.2
[49] tidyr_1.2.0 tibble_3.1.8 ggplot2_3.3.6
[52] tidyverse_1.3.2

loaded via a namespace (and not attached): [1] rsvd_1.0.5 ica_1.0-3 ps_1.7.1
[4] lmtest_0.9-40 rprojroot_2.0.3 crayon_1.5.1
[7] spatstat.core_2.4-4 MASS_7.3-58.1 nlme_3.1-160
[10] backports_1.4.1 qlcMatrix_0.9.7 reprex_2.0.2
[13] GOSemSim_2.22.0 rlang_1.0.4 XVector_0.36.0
[16] ROCR_1.0-11 readxl_1.4.1 nloptr_2.0.3
[19] callr_3.7.2 limma_3.52.2 BiocParallel_1.30.3
[22] bit64_4.0.5 glue_1.6.2 sctransform_0.3.4
[25] vipor_0.4.5 parallel_4.2.2 processx_3.7.0
[28] spatstat.sparse_2.1-1 spatstat.geom_2.4-0 haven_2.5.0
[31] tidyselect_1.1.2 usethis_2.1.6 fitdistrplus_1.1-8
[34] XML_3.99-0.10 zoo_1.8-10 xtable_1.8-4
[37] magrittr_2.0.3 cli_3.3.0 zlibbioc_1.42.0
[40] rstudioapi_0.13 miniUI_0.1.1.1 rpart_4.1.19
[43] fastmatch_1.1-3 treeio_1.20.2 shiny_1.7.2
[46] BiocSingular_1.12.0 leidenbase_0.1.11 pkgbuild_1.3.1
[49] cluster_2.1.4 tidygraph_1.2.1 KEGGREST_1.36.3
[52] ape_5.6-2 listenv_0.8.0 Biostrings_2.64.1
[55] png_0.1-7 future_1.27.0 withr_2.5.0
[58] bitops_1.0-7 slam_0.1-50 ggforce_0.3.4
[61] RBGL_1.72.0 plyr_1.8.7 cellranger_1.1.0
[64] GSEABase_1.58.0 sparsesvd_0.2 pillar_1.8.1
[67] biocViews_1.64.1 cachem_1.0.6 fs_1.5.2
[70] RUnit_0.4.32 DelayedMatrixStats_1.18.0 vctrs_0.4.1
[73] ellipsis_0.3.2 generics_0.1.3 devtools_2.4.4
[76] tools_4.2.2 beeswarm_0.4.0 munsell_0.5.0
[79] tweenr_2.0.0 fgsea_1.22.0 proxy_0.4-27
[82] DelayedArray_0.22.0 fastmap_1.1.0 compiler_4.2.2
[85] HSMMSingleCell_1.16.0 pkgload_1.3.0 abind_1.4-5
[88] httpuv_1.6.5 sessioninfo_1.2.2 plotly_4.10.0
[91] rgeos_0.5-9 GenomeInfoDbData_1.2.8 gridExtra_2.3
[94] lattice_0.20-45 deldir_1.0-6 utf8_1.2.2
[97] later_1.3.0 jsonlite_1.8.0 scales_1.2.1
[100] docopt_0.7.1 graph_1.74.0 ScaledMatrix_1.4.0
[103] tidytree_0.4.0 pbapply_1.5-0 sparseMatrixStats_1.8.0
[106] lazyeval_0.2.2 promises_1.2.0.1 R.utils_2.12.0
[109] goftest_1.2-3 spatstat.utils_2.3-1 reticulate_1.25
[112] Rtsne_0.16 downloader_0.4 uwot_0.1.13
[115] igraph_1.3.4 survival_3.4-0 htmltools_0.5.3
[118] memoise_2.0.1 profvis_0.3.7 graphlayouts_0.8.1
[121] arrow_9.0.0 digest_0.6.29 assertthat_0.2.1
[124] mime_0.12 RSQLite_2.2.16 yulab.utils_0.0.5
[127] future.apply_1.9.0 remotes_2.4.2 data.table_1.14.2
[130] urlchecker_1.0.1 blob_1.2.3 R.oo_1.25.0
[133] labeling_0.4.2 fastICA_1.2-3 googledrive_2.0.0
[136] RCurl_1.98-1.8 broom_1.0.0 hms_1.1.2
[139] modelr_0.1.9 colorspace_2.0-3 BiocManager_1.30.18
[142] ggbeeswarm_0.6.0 aplot_0.1.6 ggrastr_1.0.1
[145] Rcpp_1.0.9 RANN_2.6.1 fansi_1.0.3
[148] tzdb_0.3.0 brio_1.1.3 parallelly_1.32.1
[151] R6_2.5.1 grid_4.2.2 ggridges_0.5.3
[154] lifecycle_1.0.1 googlesheets4_1.0.1 minqa_1.2.4
[157] leiden_0.4.2 DO.db_2.9 qvalue_2.28.0
[160] desc_1.4.1 RcppAnnoy_0.0.19 htmlwidgets_1.5.4
[163] beachmat_2.12.0 polyclip_1.10-0 shadowtext_0.1.2
[166] gridGraphics_0.5-1 terra_1.6-7 rvest_1.0.3
[169] mgcv_1.8-41 globals_0.16.0 spatstat.random_2.2-0
[172] progressr_0.10.1 codetools_0.2-18 lubridate_1.8.0
[175] GO.db_3.15.0 prettyunits_1.1.1 dbplyr_2.2.1
[178] R.methodsS3_1.8.2 gtable_0.3.0 DBI_1.1.3
[181] ggfun_0.0.6 tensor_1.5 httr_1.4.4
[184] KernSmooth_2.23-20 stringi_1.7.8 reshape2_1.4.4
[187] farver_2.1.1 annotate_1.74.0 ggtree_3.4.2
[190] xml2_1.3.3 combinat_0.0-8 boot_1.3-28
[193] BiocNeighbors_1.14.0 lme4_1.1-30 ggplotify_0.1.0
[196] scattermore_0.8 bit_4.0.4 scatterpie_0.1.7
[199] spatstat.data_2.2-0 ggraph_2.0.6 pkgconfig_2.0.3
[202] babelgene_22.3 gargle_1.2.0