{"id":1068,"date":"2017-03-14T15:52:32","date_gmt":"2017-03-14T19:52:32","guid":{"rendered":"https:\/\/www.bumc.bu.edu\/kottonlab\/?page_id=1068"},"modified":"2024-12-19T13:44:28","modified_gmt":"2024-12-19T18:44:28","slug":"bioinformatics-portal-kotton-lab","status":"publish","type":"page","link":"https:\/\/www.bumc.bu.edu\/kottonlab\/bioinformatics-portal-kotton-lab\/","title":{"rendered":"Bioinformatics portal"},"content":{"rendered":"<p><img loading=\"lazy\" src=\"\/kottonlab\/files\/2017\/03\/HEAT-MAP-89x300.jpg\" alt=\"HEAT MAP\" width=\"89\" height=\"300\" class=\"size-medium wp-image-1263 alignright\" srcset=\"https:\/\/www.bumc.bu.edu\/kottonlab\/files\/2017\/03\/HEAT-MAP-89x300.jpg 89w, https:\/\/www.bumc.bu.edu\/kottonlab\/files\/2017\/03\/HEAT-MAP-768x2598.jpg 768w, https:\/\/www.bumc.bu.edu\/kottonlab\/files\/2017\/03\/HEAT-MAP-303x1024.jpg 303w, https:\/\/www.bumc.bu.edu\/kottonlab\/files\/2017\/03\/HEAT-MAP.jpg 800w\" sizes=\"(max-width: 89px) 100vw, 89px\" \/>Our laboratory performs global transcriptomic profiling to understand the genetic programs of our cells. While all our published datasets are available for free download from the gene expression omnibus (GEO), we also provide interactive websites and processed biostatistical analyses for free use through this web portal. Please enjoy and feel free to share the microarray, population-based RNA-Seq, and single cell RNA-Seq profiles below. If you find something interesting, let us know!<\/p>\n<p><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/gds\/?term=kotton\" target=\"_blank\" rel=\"noopener noreferrer\">Click here to access all our raw datasets through GEO<\/a><\/p>\n<p>Internal only: <a href=\"https:\/\/www.bumc.bu.edu\/kottonlab\/internal-list-of-datasets-crem_project_index\/\" target=\"_blank\" rel=\"noopener noreferrer\">CReM Project Index (password required)<\/a><\/p>\n<p><a href=\"\/kottonlab\/files\/2019\/03\/Summary-sheet-RNA-seq-costs.pdf\" target=\"_blank\" rel=\"noopener noreferrer\">Summary Sheet of the Kotton Lab&#8217;s sequencing approach\/costs<\/a><\/p>\n<p><em><strong>To interact with our latest microarray and single cell RNA-Seq data, click on an entry below (grouped by publication in reverse chronological order):<\/strong><\/em><\/p>\n<p>1. Interact with the shiny apps from: <span>Undeutsch HJ et al. <a href=\"https:\/\/www.cell.com\/stem-cell-reports\/fulltext\/S2213-6711(24)00292-3\">Derivation of transplantable human thyroid follicular epithelial cells from induced pluripotent stem cells<\/a> <strong>Stem Cell Reports<\/strong>.\u00a0 2024 Nov 07. <span class=\"citation-part\">PMID:\u00a0<span class=\"docsum-pmid\">39515316<\/span><\/span>\u00a0<\/span><\/p>\n<ul>\n<li><span>Figure S4 <\/span><a href=\"https:\/\/crem-bu.shinyapps.io\/scRNAseq_RA_impact_thyroid_specification\/\">https:\/\/crem-bu.shinyapps.io\/scRNAseq_RA_impact_thyroid_specification\/<\/a><\/li>\n<li><span>Figure 3 <a href=\"https:\/\/crem-bu.shinyapps.io\/scRNAseq_hiThy_timeseries_and_BMP-signaling\/\">https:\/\/crem-bu.shinyapps.io\/scRNAseq_hiThy_timeseries_and_BMP-signaling\/<\/a><\/span><\/li>\n<\/ul>\n<p>2. Interact with the shiny apps from: Burgess CL et al.\u00a0 <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38642558\/\">Generation of human alveolar epithelial type I cells from pluripotent stem cells.<\/a> <strong>Cell Stem Cell.<\/strong>2024 Apr 15. PMID: 38642558<\/p>\n<ul>\n<li><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1934590924000985?via%3Dihub#fig3\">Figure 6J<\/a> Time series scRNA-seq: <a href=\"\/kottonlab\/files\/2024\/12\/Figure-6J.-DEG.new_cluster59.xlsx\">Figure 6J. DEG.new_cluster[59]<\/a><\/li>\n<li><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1934590924000985?via%3Dihub#fig3\"><span>Figure\u00a03<\/span><\/a>\u00a0WT YAP, YAP5SA:\u00a0<a href=\"https:\/\/crem-bu.shinyapps.io\/scRNAseq_lentiviral_YAP5SA_iAT1_induction\/\"><span>https:\/\/crem-bu.shinyapps.io\/scRNAseq_lentiviral_YAP5SA_iAT1_induction\/<\/span><\/a><\/li>\n<li><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1934590924000985?via%3Dihub#fig6\"><span>Figure\u00a06<\/span><\/a>\u00a0L+DCI, YAP5SA, CKDCI:\u00a0<a href=\"https:\/\/crem-bu.shinyapps.io\/scRNAseq_iAT1_induction_methods\/\"><span>https:\/\/crem-bu.shinyapps.io\/scRNAseq_iAT1_induction_methods\/<\/span><\/a><\/li>\n<li><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1934590924000985?via%3Dihub#fig6\" data-sd-ui-side-panel-opener=\"true\" data-xocs-content-type=\"reference\" data-xocs-content-id=\"fig6\"><span>Figure\u00a06<\/span><\/a>\u00a0L+DCI Time Series:\u00a0<a href=\"https:\/\/crem-bu.shinyapps.io\/scRNAseq_iAT1_differentiation_time_series\/\"><span>https:\/\/crem-bu.shinyapps.io\/scRNAseq_iAT1_differentiation_time_series\/<\/span><\/a><\/li>\n<li><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1934590924000985?via%3Dihub#fig7\"><span>Figure\u00a07<\/span><\/a>\u00a03D vs ALI:\u00a0<a href=\"https:\/\/crem-bu.shinyapps.io\/scRNAseq_iAT1_3D_ALI_comparison\/\"><span>https:\/\/crem-bu.shinyapps.io\/scRNAseq_iAT1_3D_ALI_comparison\/<\/span><\/a><\/li>\n<\/ul>\n<p>3. Interactive data (SPRING) from: Ma L et al., <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/37625411\/\">Airway stem cell reconstitution by the transplantation of primary or pluripotent stem cell-derived basal cells<\/a>. Cell Stem Cell, 2023. PMID: 37625411<\/p>\n<ul>\n<li>Figure 1: In vitro iBC culture<a href=\"https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/20_10_08_martin\/D129_DSi\">:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/20_10_08_martin\/D129_DSi<\/a><\/li>\n<li>Figure 2: Murine primary BC transplantation into syngeneic immunocompetent mouse tracheae<a href=\"https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/21_12_17_martin\/Primary_Epi_Only\">:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/21_12_17_martin\/Primary_Epi_Only<\/a><\/li>\n<li>Figure 4: Murine iBC transplantation into syngeneic immunocompetent mouse trachea <a href=\"https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/22_01_05_martin_iBC\/iBC_merged_Epi\">:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/22_01_05_martin_iBC\/iBC_merged_Epi<\/a><\/li>\n<li>Figure 6: Murine iBC serial secondary transplantation 5<sup>th<\/sup> gen recipient trachea:<a href=\"https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/22_\">https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/22_<\/a><\/li>\n<li>Figure 6: Murine iBC serial secondary transplantation 5<sup>th<\/sup> gen recipient data merged with 1<sup>st<\/sup> gen recipient data: <a href=\"https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/22_09_16_martin_combined_with_previous\/Epi_only\">https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/22_09_16_martin_combined_with_previous\/Epi_only<\/a><\/li>\n<li>Figure 7: Human primary BC and iBC transplantation into immunodeficient mouse trachea: <a href=\"https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/combined_allHuman_withNGPT\/combined_allHuman_withNGPT\">https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/combined_allHuman_withNGPT\/combined_allHuman_withNGPT<\/a><\/li>\n<\/ul>\n<p>4. Interactive data (SPRING) from: Herriges MJ et al., <a href=\"https:\/\/www.cell.com\/cell-stem-cell\/fulltext\/S1934-5909(23)00283-7\">Durable alveolar engraftment of PSC-derived lung epithelial cells into immunocompetent mice<\/a> Cell Stem Cell, 2023. PMID: 37625412<\/p>\n<ul>\n<li>Figure 2: Primary and ESC-derived tip-like cells: <a href=\"https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/21_01_06_herriges_LPM_ESC_and_Primary\/21_01_06_herriges_LPM_ESC_and_Primary\">https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/21_01_06_herriges_LPM_ESC_and_Primary\/21_01_06_herriges_LPM_ESC_and_Primary<\/a><\/li>\n<li>Figure 4: 6- and 15-weeks post-transplantation of ESC-derived tip-like cells\n<ul>\n<li style=\"text-align: justify;\">Cluster labels:<\/li>\n<li>2: AT1 and AT1-like cells<\/li>\n<li>4: Ciliated cells<\/li>\n<li>6: Basal cells<\/li>\n<li>7: Gastric-like cells<\/li>\n<li>8: Neuroendocrine cells<\/li>\n<li>0+: AT2 cells<\/li>\n<li>1+13: Secretory cells<\/li>\n<li>3+14: AT2-like cells<\/li>\n<li><a href=\"https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/21_01_06_herriges_with_week6_invivo\/everything2\">https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/21_01_06_herriges_with_week6_invivo\/everything2<\/a><\/li>\n<\/ul>\n<\/li>\n<li>Supp. Figure 6: 8- weeks post-transplantation of primary or ESC-derived tip-like cells\n<ul>\n<li>Cluster labels (At Res 0.5):<\/li>\n<li>0,7,11: Primary AT2-like cells<\/li>\n<li>1,2,8: AT2 cells<\/li>\n<li>3,12: Ciliated cells<\/li>\n<li>4: AT1-like cells<\/li>\n<li>5: ESC-derived AT2-like cells<\/li>\n<li>6: Secretory cells<\/li>\n<li>9: AT1 cells<\/li>\n<li>10: Basal cells<\/li>\n<li>13: Fibroblasts<\/li>\n<li>14: Gastric-like cells<\/li>\n<li>15: Neuroendocrine cells<\/li>\n<li><a href=\"https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/22_08_31_michael_new\/22_08_31_michael_new\">https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/22_08_31_michael_new\/22_08_31_michael_new<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p><a href=\"https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/combined_allHuman_withNGPT\/combined_allHuman_withNGPT\"><\/a>5. <a href=\"https:\/\/crem-bu.shinyapps.io\/scRNAseq-AEC2-comparisons\/\">Interactive ShinyApp (human primary\/cultured AT2s and iAT2s)<\/a> from: <span>Alysandratos KD et al.\u00a0<\/span><a class=\"docsum-title\" href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/36454643\/\" ref=\"linksrc=docsum_link&amp;article_id=36454643&amp;ordinalpos=1&amp;page=1\" data-ga-category=\"result_click\" data-ga-action=\"1\" data-ga-label=\"36454643\" data-full-article-url=\"from_term=alysandratos+kotton+jci&amp;from_sort=date&amp;from_size=50&amp;from_pos=1\" data-article-id=\"36454643\">Culture impact on the transcriptomic programs of primary and iPSC-derived human alveolar type 2 cells.<span>\u00a0<\/span><\/a><span class=\"docsum-journal-citation full-journal-citation\"><strong>JCI Insight<\/strong>. 2023 Jan 10.<span>\u00a0<\/span><\/span><span class=\"citation-part\">PMID:\u00a0<span class=\"docsum-pmid\">36454643<\/span><\/span><\/p>\n<p>6. <a href=\"https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/19_12_06_kristy\/19_12_06_kristy\" target=\"_blank\" rel=\"noopener noreferrer\">Interactive data (SPRING plot)<\/a> from <strong>Abo et al. JCI Insight 2022.<\/strong>\u00a0 <strong><a href=\"https:\/\/insight.jci.org\/articles\/view\/155589\">Air-liquid interface culture promotes maturation and allows environmental exposure of pluripotent stem cell\u2013derived alveolar epithelium<\/a><\/strong>. SPRING from Figure 4 (scRNA-seq of SPC2 iAEC2 cells in 3D, 2D, ALI, and smoked ALI cultures).<\/p>\n<p>7. Interactive data from <strong>Alysandratos et al. Cell Reports 2021<\/strong>. <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/34469722\/\" target=\"_blank\" rel=\"noopener noreferrer\"><strong>Patient-specific iPSCs carrying an SFTPC mutation reveal the intrinsic alveolar epithelial dysfunction at the inception of interstitial lung disease<\/strong>.<\/a>:<\/p>\n<ul>\n<li><a href=\"https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/20_08_13_kostas_D30_D113\/20_08_13_kostas_D30_D113\" target=\"_blank\" rel=\"noopener noreferrer\">Interact with data from Fig. 4 (SPRING plot of day 30 and day 113 of differentiation of SFTPCI73T mutant (I73T\/tdT) vs corrected (tdT\/WT)\u00a0 iAEC2s.<\/a><\/li>\n<li><a href=\"http:\/\/165.123.69.6\/website\/scrna.html\" target=\"_blank\" rel=\"noopener noreferrer\">Interact with UMAP data from Fig S3 (via our U01 IPF Consortium site)<\/a>.<\/li>\n<li><a href=\"https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/18_03_21_kostas_comb\/18_03_21_kostas_comb\" target=\"_blank\" rel=\"noopener noreferrer\">Interact with data from Fig S3 (SPRING plot of day 114 of differentiation SFTPCI73T mutant (clone C11) vs corrected (clone B2) iAEC2s.<\/a><\/li>\n<\/ul>\n<p>8.Interactive data from<strong> <a href=\"https:\/\/www.cell.com\/cell-stem-cell\/fulltext\/S1934-5909(20)30492-6\" target=\"_blank\" rel=\"noopener noreferrer\">Hawkins, Suzuki et al. Cell Stem Cell. 2020<\/a>.<\/strong> <strong>Derivation of Airway Basal Stem Cells from Human Pluripotent Stem Cells<\/strong>:<\/p>\n<ul>\n<li><a href=\"https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/Hawkins2020_Fig2E_Differentiation_2_media\/Hawkins2020_Fig2E_Differentiation_2_media\" target=\"_blank\" rel=\"noopener noreferrer\">Interact with data from Fig 2E (SPRING plot of Media effect in 3D iPSC-ariway culture)<\/a><\/li>\n<li><a href=\"https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/Hawkins2020_Fig4A_iBC-derived_ALI\/Hawkins2020_Fig4A_iBC-derived_ALI\" target=\"_blank\" rel=\"noopener noreferrer\">Interact with data from Fig 4A (SPRING plot of BU3 NGPT iBCs after differentiation in ALI culture)<\/a><\/li>\n<li><a href=\"https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/19_06_17_hawkins_FH_BU3NGPT-ALI\/19_06_17_hawkins_FH_BU3NGPT-ALI\" target=\"_blank\" rel=\"noopener noreferrer\"><span style=\"font-weight: 400;\">Additional SPRING plot of scRNA-seq of BU3 NGPT ALI culture via SPRING here<\/span><\/a><\/li>\n<\/ul>\n<p>9.Interactive data from <a href=\"https:\/\/www.cell.com\/cell-stem-cell\/fulltext\/S1934-5909(20)30459-8\" target=\"_blank\" rel=\"noopener noreferrer\"><strong>Huang et al. Cell Stem Cell. Sept 2020<\/strong><\/a>: <strong>SARS-CoV-2 Infection of Pluripotent Stem Cell-derived Human Lung Alveolar Type 2 Cells Elicits a Rapid Epithelial-Intrinsic Inflammatory Response.<\/strong><\/p>\n<ul>\n<li><a href=\"\/kottonlab\/files\/2020\/09\/Table-S1.xlsx\">Download RNA-Seq table S1<\/a> (Excel: Differentially Expressed Genes in iAT2s after SARS-CoV-2 infection).<\/li>\n<li><a href=\"https:\/\/crem.shinyapps.io\/SARS-CoV-2-infected-AT2\/\" target=\"_blank\" rel=\"noopener noreferrer\">View the interactive ShinyApp<\/a> and type in your favorite gene to see how it changes in infected iAT2s (Kotton Lab) as well as in primary adult human cultured AT2s (Tata Lab)!<\/li>\n<\/ul>\n<p>10. Interactive data from <strong><span>Hurley et al 2020. <\/span><a href=\"https:\/\/www.cell.com\/cell-stem-cell\/fulltext\/S1934-5909(19)30527-2\" target=\"_blank\" rel=\"noopener noreferrer\">Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors<\/a><span>.<\/span><\/strong><\/p>\n<ul>\n<li><a href=\"\/kottonlab\/files\/2020\/01\/Table-S1-Hurley-CSC-2020.xlsx\" target=\"_blank\" rel=\"noopener noreferrer\">Download primary human fetal through adult lung AEC2 RNA Seq data<\/a> (week 16 gestation through adult; top 1000 most varying genes; from our paper&#8217;s figure 1; Table S1.xls)<\/li>\n<li><a href=\"https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?cgi-bin\/client_datasets\/nacho_springplot\/allMerged\" target=\"_blank\" rel=\"noopener noreferrer\">View the SPRING plot (from figure 3; our human iPSC distal lung directed differentiation scRNA Seq time series)<\/a> &#8212; and search for your favorite gene!<\/li>\n<li><a href=\"http:\/\/jund.andrew.cmu.edu:8080\/bu_lung\/bu_lung_cshmm\/viz.html\" target=\"_blank\" rel=\"noopener noreferrer\">View Jun Ding&#8217;s interactive on line tool from figure 4<\/a> and follow the branching cell fate trajectories in our Continuous State Hidden Markov Model<\/li>\n<li><a href=\"https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/day_114_SPC2-B2_iAEC2s\/day_114_SPC2-B2_iAEC2s\" target=\"_blank\" rel=\"noopener noreferrer\">View the SPRING plot (from figure 7; scRNA Seq for our human iPSC-derived AEC2 that are 114 days in culture)<\/a> &#8212; and search for your favorite gene!<\/li>\n<li><a href=\"https:\/\/kleintools.hms.harvard.edu\/tools\/springViewer_1_6_dev.html?client_datasets\/lineage_traced_iAEC2_day_27\/lineage_traced_iAEC2_day_27\" target=\"_blank\" rel=\"noopener noreferrer\">View the SPRING plot (from figure S5; lineage tracing of iPSC-Derived AEC2 with lentiviral barcoding and subsequent scRNA-seq )<\/a> &#8212; and search for your favorite gene!<\/li>\n<\/ul>\n<p>11. Interactive data from <strong><a href=\"https:\/\/www.nature.com\/articles\/s41467-020-14348-3\" target=\"_blank\" rel=\"noopener noreferrer\">Ikonomou et al. Nature Communications. Jan 2020<\/a>:\u00a0The in vivo genetic program of Primordial Lung Progenitors (E9.0 mouse):<\/strong><\/p>\n<ul>\n<li><a href=\"\/kottonlab\/files\/2020\/02\/Supplemental-table-1.xlsx\">Download RNA seq, pairwise comparisons (28MB excel file; Table S1)<\/a>\u00a0from figure 3 of lung, thyroid, forebrain and their endodermal\/ectodermal precursors <strong>in vivo<\/strong>.<\/li>\n<li><a href=\"\/kottonlab\/files\/2020\/02\/Figure-5h-D14-mESC-bulk-RNA-seq-comparisons.xlsx\">Download RNA seq comparisons of <strong>in vitro<\/strong> mESC-derived day 14 progenitors from figure 5h<\/a> (6MB excel file: Figure 5h).<\/li>\n<\/ul>\n<p>12. Query your favorite gene in the scRNA-Seq datasets for our human iPSC-derived bronchospheres and alveolospheres, published in <a href=\"http:\/\/www.cell.com\/stem-cell-reports\/fulltext\/S2213-6711(18)30140-1\" target=\"_blank\" rel=\"noopener noreferrer\"><strong>McCauley et al Stem Cell Reports, April 2018.<\/strong><\/a> <strong>Single cell Transcriptomic Profiling of Pluripotent Stem Cell-Derived SCGB3A2+ Airway epithelium.<\/strong><\/p>\n<ul>\n<li><a href=\"https:\/\/research.cchmc.org\/pbge\/lunggens\/lungExternal\/scgb3a2_timecourse.html\" target=\"_blank\" rel=\"noopener noreferrer\">Figure 3 interactive data<\/a>: Time series Microarray of RUES2 SCGB3A2 Cherry picker ESC line: proximal differentiation through day 36 (analysis via LGEA)<\/li>\n<li><a href=\"https:\/\/research.cchmc.org\/pbge\/lunggens\/lungExternal\/genequery_scgb3a2.html\" target=\"_blank\" rel=\"noopener noreferrer\">Figure 5 interactive data<\/a>: scRNA seq (Fluidigm C1), RUES2 SCGB3A2 Cherry Picker ESC line. Day 27 proximal differentiation (analysis via LGEA).<\/li>\n<li><a href=\"https:\/\/research.cchmc.org\/pbge\/lunggens\/lungExternal\/genequery_scgb3a2_dp.html\" target=\"_blank\" rel=\"noopener noreferrer\">Figure 6 interactive data<\/a>: scRNA-seq of day 41 proximal vs distal media (BU3 NGST line; analysis via LGEA).<\/li>\n<li><a href=\"\/kottonlab\/files\/2018\/04\/Loupe-viewing-instructions.docx\">Loupe viewing instructions<\/a>. <a href=\"https:\/\/drive.google.com\/file\/d\/14IOZWx1aBKOqn7eo8IZ32d7IH872AWUd\/view?usp=sharing\" target=\"_blank\" rel=\"noopener noreferrer\">Download loupe file (43MB)<\/a>, or access the raw data via GEO:<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE103920\" target=\"_blank\" rel=\"noopener noreferrer\">GSE103920<\/a> (10x Chromium and Fluidigm data) or\u00a0<span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE103517\" target=\"_blank\" rel=\"noopener noreferrer\">GSE103517<\/a> (Affymetrix microarray),\u00a0<\/span><\/li>\n<\/ul>\n<p>13. Access our RNA-Seq data from our <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=gse96642\" target=\"_blank\" rel=\"noopener noreferrer\">time series including iAEC2s, published by <strong>Jacob et al in Cell Stem Cell 2017<\/strong><\/a><\/p>\n<p>14. Download an excel file (42MB) with human iPSC time-series biostatistics from our <a href=\"\/kottonlab\/files\/2017\/03\/2015-02-04_Kotton_analysis.xlsx\" style=\"color: #0000ff;\" target=\"_blank\" rel=\"noopener noreferrer\">Microarray profiling of major <\/a><a href=\"\/kottonlab\/files\/2017\/03\/2015-02-04_Kotton_analysis.xlsx\">stages of the lung directed differentiation protocol<\/a>\u00a0(published in <a href=\"https:\/\/www.jci.org\/articles\/view\/89950\" target=\"_blank\" rel=\"noopener noreferrer\">Hawkins et al. JCI 2017<\/a>.)<\/p>\n<p><em><strong>15. Interact with our human iPSC-derived lung single cell RNA-Seq<\/strong><\/em> analyses through either:<\/p>\n<p>A: The\u00a0<a href=\"https:\/\/research.cchmc.org\/pbge\/lunggens\/mainportal.html\" target=\"_blank\" rel=\"noopener noreferrer\">Cincinnati LGEA (Lung Gene Expression Analysis) web portal<\/a>\u00a0or&#8230;<\/p>\n<p>B:\u00a0<a href=\"https:\/\/iandriver.shinyapps.io\/ips17-bu3_single_cell_data\/\" target=\"_blank\" rel=\"noopener noreferrer\">Ian Driver&#8217;s interactive Monocle tool<\/a> to look up your favorite gene in our published Monocle analysis of iPSC-derived NKX2-1+ lung progenitors (Hawkins JCI 2017; BE SURE TO TYPE YOUR GENE NAME IN CAPS ONLY).<\/p>\n<p><strong>Other analyses from our published papers:<\/strong><\/p>\n<ol>\n<li>Mouse ESC-derived Nkx2-1+ sorted lung vs thyroid progenitors (<a href=\"\/kottonlab\/files\/2020\/03\/2016-09-22_Kotton_clustersList_for_paper.xlsx\">Download 1MB Affy array excel file<\/a> from figure 4 of\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28947536\" target=\"_blank\" rel=\"noopener noreferrer\">Serra\/Kotton. Development 2017<\/a>)<\/li>\n<li><strong>hiPSC\/ESC hepatic directed differentiation time series analyses<\/strong> (Affy arrays): as published in <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/25843048\" target=\"_blank\" rel=\"noopener noreferrer\">Wilson\/Kotton Stem Cell Reports 2015<\/a>. Download an <a href=\"\/kottonlab\/files\/2017\/05\/time_results.xls\" target=\"_blank\" rel=\"noopener noreferrer\">an excel file<\/a> of the time series computational analysis (33MB). Or <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE66076\" target=\"_blank\" rel=\"noopener noreferrer\">access the GEO raw data.<\/a><\/li>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/sites\/GDSbrowser?acc=GDS3904\" target=\"_blank\" rel=\"noopener noreferrer\">Mouse ESC\/iPSC definitive endoderm directed differentiation<\/a>\u00a0(Christodoulou, JCI 2011)<\/li>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/sites\/GDSbrowser?acc=GDS3904\" target=\"_blank\" rel=\"noopener noreferrer\">Mouse in vivo fetal developing definitive endoderm<\/a><\/li>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE49231\" target=\"_blank\" rel=\"noopener noreferrer\">Human clone to clone hiPSC variability: impact on blood differentiation efficiency<\/a><\/li>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE35063\" target=\"_blank\" rel=\"noopener noreferrer\">Mouse ESC derived Nkx2-1GFP mixed lung\/thyroid cells<\/a> (Longmire\/Kotton Cell Stem Cell 2012).<\/li>\n<\/ol>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Our laboratory performs global transcriptomic profiling to understand the genetic programs of our cells. While all our published datasets are available for free download from the gene expression omnibus (GEO), we also provide interactive websites and processed biostatistical analyses for free use through this web portal. Please enjoy and feel free to share the microarray, [&hellip;]<\/p>\n","protected":false},"author":1319,"featured_media":0,"parent":0,"menu_order":10,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/www.bumc.bu.edu\/kottonlab\/wp-json\/wp\/v2\/pages\/1068"}],"collection":[{"href":"https:\/\/www.bumc.bu.edu\/kottonlab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.bumc.bu.edu\/kottonlab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/kottonlab\/wp-json\/wp\/v2\/users\/1319"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/kottonlab\/wp-json\/wp\/v2\/comments?post=1068"}],"version-history":[{"count":51,"href":"https:\/\/www.bumc.bu.edu\/kottonlab\/wp-json\/wp\/v2\/pages\/1068\/revisions"}],"predecessor-version":[{"id":2814,"href":"https:\/\/www.bumc.bu.edu\/kottonlab\/wp-json\/wp\/v2\/pages\/1068\/revisions\/2814"}],"wp:attachment":[{"href":"https:\/\/www.bumc.bu.edu\/kottonlab\/wp-json\/wp\/v2\/media?parent=1068"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}