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prolong gold antifade mountant with dna stain dapi  (Thermo Fisher)


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    Thermo Fisher prolong gold antifade mountant with dna stain dapi
    Prolong Gold Antifade Mountant With Dna Stain Dapi, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/prolong%E2%84%A2+gold+antifade+mountant+with+dapi/prolong+diamond+antifade+mountant/pmc12276352-371-16-19
    Average 90 stars, based on 1 article reviews
    prolong gold antifade mountant with dna stain dapi - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    Saline:

    Article Title: ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Article Snippet: Cat# 130-106-549 bFGF R&D system Cat# 233-FB-025 Activing A Peprotech Cat# 120-14E-10 Gelatin Millipore Cat# ES-006-B Bovine plasma fibronectin Sigma Cat# F1141 Accutase Sigma Cat# A6964 Nuclei EZ lysis buffer Sigma Cat# N3408 Pierce protease inhibitor, EDTA-free ThermoFisher Cat# A32965 Proteinase K Ambion Cat# AM2546 ProLongTM Gold Antifade Mountant with DAPI ThermoFisher Cat# P36941 Critical Commercial Assays QIAshredder RNA Extraction Column QIAGEN Cat# 79654 RNeasy Plus Mini Kit QIAGEN Cat# 74134 RNase-free DNase set QIAGEN Cat# 79254 miniElute Reaction Cleanup QIAGEN Cat# 28204 TruSeq RNA library kit v2 Illumina Cat# RS-122-2001 Nextera DNA library Prep kit Illumina Cat# FC-121-1031 Nextera Index kit Illumina Cat# FC-121-1012 NEBNext high fidelity 2x PCR master mix NEB Cat# M0541 Ampure XP beads Beckman Coulter Agencourt Cat# A63881 Leukocyte Alkaline Phosphatase kit Sigma Cat# 86R-1KT Deposited Data ATAC-seq ArrayExpress ArrayExpress: E-MTAB-7207 ChIPmentation-seq ArrayExpress ArrayExpress: E-MTAB-7208 RNA-seq ArrayExpress ArrayExpress: E-MTAB-7206 Single cell (sc) RNA-seq ArrayExpress ArrayExpress: E-MTAB-7211 Experimental Models: Cell Lines Mouse Rex1GFPd2 ES cells Yang et al., 2012 N/A (Continued on next page) e1 Cell Reports 27, 3215–3227.e1–e6, June 11, 2019

    Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells
    Article Snippet: 2007 https://matplotlib.org/index.html Seaborn 0.9.0 https://seaborn.pydata.org/# Enrichr in gseapy 0.9.13 Kuleshov et al. 2016 https://github.com/zqfang/GSEApy/blob/master/docs/index.rst Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 van Dijk et al. 2018 https://github.com/KrishnaswamyLab/MAGIC Other ProLongTM Gold Antifade Mountant with DAPI Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"P36935","term_id":"549826","term_text":"P36935"}} P36935 DAPI Sigma-Aldrich Cat#D9542 Transwells Corning Cat#3470 SPRI Select Reagent Beckman Coulter Cat#NC0406407 QubitTM dsDNA HS Assay Kit Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Calcein Blue AM Life Technologies Cat#C1429 Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) Gibco Cat#14175095 Gentle Cell Dissociation Reagent StemCell Technologies Cat#07174 GlutaMAX (100x) Thermo Fisher Scientific Cat#35050–061 Ham’s F12 Medium Cellgro Cat#10–080-CV Iscove’s Modified Dulbecco’s Medium(IMDM) Thermo Fisher Scientific Cat#12440053 N2 Supplement Invitrogen Cat#17502–048 B27 Supplement Invitrogen Cat#15260–037 Primocin Invitrogen Cat#NC9141851 mTeSR1 StemCell Technologies Cat#05850 Open in a separate window KEY RESOURCES TABLE Alveolar progenitor (AT2) cells are transcriptionally distinct upon KRAS expression Alveolar epithelial organoids recapitulate early-stage lung adenocarcinoma Oncogenic KRAS leads to loss of lineage identity in AT2 cells Bulk, scRNAseq, and proteomic data from murine and human KRAS mutant AT2 cells

    Gentle:

    Article Title: ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Article Snippet: Cat# 130-106-549 bFGF R&D system Cat# 233-FB-025 Activing A Peprotech Cat# 120-14E-10 Gelatin Millipore Cat# ES-006-B Bovine plasma fibronectin Sigma Cat# F1141 Accutase Sigma Cat# A6964 Nuclei EZ lysis buffer Sigma Cat# N3408 Pierce protease inhibitor, EDTA-free ThermoFisher Cat# A32965 Proteinase K Ambion Cat# AM2546 ProLongTM Gold Antifade Mountant with DAPI ThermoFisher Cat# P36941 Critical Commercial Assays QIAshredder RNA Extraction Column QIAGEN Cat# 79654 RNeasy Plus Mini Kit QIAGEN Cat# 74134 RNase-free DNase set QIAGEN Cat# 79254 miniElute Reaction Cleanup QIAGEN Cat# 28204 TruSeq RNA library kit v2 Illumina Cat# RS-122-2001 Nextera DNA library Prep kit Illumina Cat# FC-121-1031 Nextera Index kit Illumina Cat# FC-121-1012 NEBNext high fidelity 2x PCR master mix NEB Cat# M0541 Ampure XP beads Beckman Coulter Agencourt Cat# A63881 Leukocyte Alkaline Phosphatase kit Sigma Cat# 86R-1KT Deposited Data ATAC-seq ArrayExpress ArrayExpress: E-MTAB-7207 ChIPmentation-seq ArrayExpress ArrayExpress: E-MTAB-7208 RNA-seq ArrayExpress ArrayExpress: E-MTAB-7206 Single cell (sc) RNA-seq ArrayExpress ArrayExpress: E-MTAB-7211 Experimental Models: Cell Lines Mouse Rex1GFPd2 ES cells Yang et al., 2012 N/A (Continued on next page) e1 Cell Reports 27, 3215–3227.e1–e6, June 11, 2019

    Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells
    Article Snippet: 2007 https://matplotlib.org/index.html Seaborn 0.9.0 https://seaborn.pydata.org/# Enrichr in gseapy 0.9.13 Kuleshov et al. 2016 https://github.com/zqfang/GSEApy/blob/master/docs/index.rst Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 van Dijk et al. 2018 https://github.com/KrishnaswamyLab/MAGIC Other ProLongTM Gold Antifade Mountant with DAPI Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"P36935","term_id":"549826","term_text":"P36935"}} P36935 DAPI Sigma-Aldrich Cat#D9542 Transwells Corning Cat#3470 SPRI Select Reagent Beckman Coulter Cat#NC0406407 QubitTM dsDNA HS Assay Kit Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Calcein Blue AM Life Technologies Cat#C1429 Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) Gibco Cat#14175095 Gentle Cell Dissociation Reagent StemCell Technologies Cat#07174 GlutaMAX (100x) Thermo Fisher Scientific Cat#35050–061 Ham’s F12 Medium Cellgro Cat#10–080-CV Iscove’s Modified Dulbecco’s Medium(IMDM) Thermo Fisher Scientific Cat#12440053 N2 Supplement Invitrogen Cat#17502–048 B27 Supplement Invitrogen Cat#15260–037 Primocin Invitrogen Cat#NC9141851 mTeSR1 StemCell Technologies Cat#05850 Open in a separate window KEY RESOURCES TABLE Alveolar progenitor (AT2) cells are transcriptionally distinct upon KRAS expression Alveolar epithelial organoids recapitulate early-stage lung adenocarcinoma Oncogenic KRAS leads to loss of lineage identity in AT2 cells Bulk, scRNAseq, and proteomic data from murine and human KRAS mutant AT2 cells

    Modification:

    Article Title: ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Article Snippet: Cat# 130-106-549 bFGF R&D system Cat# 233-FB-025 Activing A Peprotech Cat# 120-14E-10 Gelatin Millipore Cat# ES-006-B Bovine plasma fibronectin Sigma Cat# F1141 Accutase Sigma Cat# A6964 Nuclei EZ lysis buffer Sigma Cat# N3408 Pierce protease inhibitor, EDTA-free ThermoFisher Cat# A32965 Proteinase K Ambion Cat# AM2546 ProLongTM Gold Antifade Mountant with DAPI ThermoFisher Cat# P36941 Critical Commercial Assays QIAshredder RNA Extraction Column QIAGEN Cat# 79654 RNeasy Plus Mini Kit QIAGEN Cat# 74134 RNase-free DNase set QIAGEN Cat# 79254 miniElute Reaction Cleanup QIAGEN Cat# 28204 TruSeq RNA library kit v2 Illumina Cat# RS-122-2001 Nextera DNA library Prep kit Illumina Cat# FC-121-1031 Nextera Index kit Illumina Cat# FC-121-1012 NEBNext high fidelity 2x PCR master mix NEB Cat# M0541 Ampure XP beads Beckman Coulter Agencourt Cat# A63881 Leukocyte Alkaline Phosphatase kit Sigma Cat# 86R-1KT Deposited Data ATAC-seq ArrayExpress ArrayExpress: E-MTAB-7207 ChIPmentation-seq ArrayExpress ArrayExpress: E-MTAB-7208 RNA-seq ArrayExpress ArrayExpress: E-MTAB-7206 Single cell (sc) RNA-seq ArrayExpress ArrayExpress: E-MTAB-7211 Experimental Models: Cell Lines Mouse Rex1GFPd2 ES cells Yang et al., 2012 N/A (Continued on next page) e1 Cell Reports 27, 3215–3227.e1–e6, June 11, 2019

    Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells
    Article Snippet: 2007 https://matplotlib.org/index.html Seaborn 0.9.0 https://seaborn.pydata.org/# Enrichr in gseapy 0.9.13 Kuleshov et al. 2016 https://github.com/zqfang/GSEApy/blob/master/docs/index.rst Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 van Dijk et al. 2018 https://github.com/KrishnaswamyLab/MAGIC Other ProLongTM Gold Antifade Mountant with DAPI Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"P36935","term_id":"549826","term_text":"P36935"}} P36935 DAPI Sigma-Aldrich Cat#D9542 Transwells Corning Cat#3470 SPRI Select Reagent Beckman Coulter Cat#NC0406407 QubitTM dsDNA HS Assay Kit Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Calcein Blue AM Life Technologies Cat#C1429 Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) Gibco Cat#14175095 Gentle Cell Dissociation Reagent StemCell Technologies Cat#07174 GlutaMAX (100x) Thermo Fisher Scientific Cat#35050–061 Ham’s F12 Medium Cellgro Cat#10–080-CV Iscove’s Modified Dulbecco’s Medium(IMDM) Thermo Fisher Scientific Cat#12440053 N2 Supplement Invitrogen Cat#17502–048 B27 Supplement Invitrogen Cat#15260–037 Primocin Invitrogen Cat#NC9141851 mTeSR1 StemCell Technologies Cat#05850 Open in a separate window KEY RESOURCES TABLE Alveolar progenitor (AT2) cells are transcriptionally distinct upon KRAS expression Alveolar epithelial organoids recapitulate early-stage lung adenocarcinoma Oncogenic KRAS leads to loss of lineage identity in AT2 cells Bulk, scRNAseq, and proteomic data from murine and human KRAS mutant AT2 cells

    Expressing:

    Article Title: ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Article Snippet: Cat# 130-106-549 bFGF R&D system Cat# 233-FB-025 Activing A Peprotech Cat# 120-14E-10 Gelatin Millipore Cat# ES-006-B Bovine plasma fibronectin Sigma Cat# F1141 Accutase Sigma Cat# A6964 Nuclei EZ lysis buffer Sigma Cat# N3408 Pierce protease inhibitor, EDTA-free ThermoFisher Cat# A32965 Proteinase K Ambion Cat# AM2546 ProLongTM Gold Antifade Mountant with DAPI ThermoFisher Cat# P36941 Critical Commercial Assays QIAshredder RNA Extraction Column QIAGEN Cat# 79654 RNeasy Plus Mini Kit QIAGEN Cat# 74134 RNase-free DNase set QIAGEN Cat# 79254 miniElute Reaction Cleanup QIAGEN Cat# 28204 TruSeq RNA library kit v2 Illumina Cat# RS-122-2001 Nextera DNA library Prep kit Illumina Cat# FC-121-1031 Nextera Index kit Illumina Cat# FC-121-1012 NEBNext high fidelity 2x PCR master mix NEB Cat# M0541 Ampure XP beads Beckman Coulter Agencourt Cat# A63881 Leukocyte Alkaline Phosphatase kit Sigma Cat# 86R-1KT Deposited Data ATAC-seq ArrayExpress ArrayExpress: E-MTAB-7207 ChIPmentation-seq ArrayExpress ArrayExpress: E-MTAB-7208 RNA-seq ArrayExpress ArrayExpress: E-MTAB-7206 Single cell (sc) RNA-seq ArrayExpress ArrayExpress: E-MTAB-7211 Experimental Models: Cell Lines Mouse Rex1GFPd2 ES cells Yang et al., 2012 N/A (Continued on next page) e1 Cell Reports 27, 3215–3227.e1–e6, June 11, 2019

    Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells
    Article Snippet: 2007 https://matplotlib.org/index.html Seaborn 0.9.0 https://seaborn.pydata.org/# Enrichr in gseapy 0.9.13 Kuleshov et al. 2016 https://github.com/zqfang/GSEApy/blob/master/docs/index.rst Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 van Dijk et al. 2018 https://github.com/KrishnaswamyLab/MAGIC Other ProLongTM Gold Antifade Mountant with DAPI Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"P36935","term_id":"549826","term_text":"P36935"}} P36935 DAPI Sigma-Aldrich Cat#D9542 Transwells Corning Cat#3470 SPRI Select Reagent Beckman Coulter Cat#NC0406407 QubitTM dsDNA HS Assay Kit Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Calcein Blue AM Life Technologies Cat#C1429 Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) Gibco Cat#14175095 Gentle Cell Dissociation Reagent StemCell Technologies Cat#07174 GlutaMAX (100x) Thermo Fisher Scientific Cat#35050–061 Ham’s F12 Medium Cellgro Cat#10–080-CV Iscove’s Modified Dulbecco’s Medium(IMDM) Thermo Fisher Scientific Cat#12440053 N2 Supplement Invitrogen Cat#17502–048 B27 Supplement Invitrogen Cat#15260–037 Primocin Invitrogen Cat#NC9141851 mTeSR1 StemCell Technologies Cat#05850 Open in a separate window KEY RESOURCES TABLE Alveolar progenitor (AT2) cells are transcriptionally distinct upon KRAS expression Alveolar epithelial organoids recapitulate early-stage lung adenocarcinoma Oncogenic KRAS leads to loss of lineage identity in AT2 cells Bulk, scRNAseq, and proteomic data from murine and human KRAS mutant AT2 cells

    Mutagenesis:

    Article Title: ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Article Snippet: Cat# 130-106-549 bFGF R&D system Cat# 233-FB-025 Activing A Peprotech Cat# 120-14E-10 Gelatin Millipore Cat# ES-006-B Bovine plasma fibronectin Sigma Cat# F1141 Accutase Sigma Cat# A6964 Nuclei EZ lysis buffer Sigma Cat# N3408 Pierce protease inhibitor, EDTA-free ThermoFisher Cat# A32965 Proteinase K Ambion Cat# AM2546 ProLongTM Gold Antifade Mountant with DAPI ThermoFisher Cat# P36941 Critical Commercial Assays QIAshredder RNA Extraction Column QIAGEN Cat# 79654 RNeasy Plus Mini Kit QIAGEN Cat# 74134 RNase-free DNase set QIAGEN Cat# 79254 miniElute Reaction Cleanup QIAGEN Cat# 28204 TruSeq RNA library kit v2 Illumina Cat# RS-122-2001 Nextera DNA library Prep kit Illumina Cat# FC-121-1031 Nextera Index kit Illumina Cat# FC-121-1012 NEBNext high fidelity 2x PCR master mix NEB Cat# M0541 Ampure XP beads Beckman Coulter Agencourt Cat# A63881 Leukocyte Alkaline Phosphatase kit Sigma Cat# 86R-1KT Deposited Data ATAC-seq ArrayExpress ArrayExpress: E-MTAB-7207 ChIPmentation-seq ArrayExpress ArrayExpress: E-MTAB-7208 RNA-seq ArrayExpress ArrayExpress: E-MTAB-7206 Single cell (sc) RNA-seq ArrayExpress ArrayExpress: E-MTAB-7211 Experimental Models: Cell Lines Mouse Rex1GFPd2 ES cells Yang et al., 2012 N/A (Continued on next page) e1 Cell Reports 27, 3215–3227.e1–e6, June 11, 2019

    Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells
    Article Snippet: 2007 https://matplotlib.org/index.html Seaborn 0.9.0 https://seaborn.pydata.org/# Enrichr in gseapy 0.9.13 Kuleshov et al. 2016 https://github.com/zqfang/GSEApy/blob/master/docs/index.rst Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 van Dijk et al. 2018 https://github.com/KrishnaswamyLab/MAGIC Other ProLongTM Gold Antifade Mountant with DAPI Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"P36935","term_id":"549826","term_text":"P36935"}} P36935 DAPI Sigma-Aldrich Cat#D9542 Transwells Corning Cat#3470 SPRI Select Reagent Beckman Coulter Cat#NC0406407 QubitTM dsDNA HS Assay Kit Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Calcein Blue AM Life Technologies Cat#C1429 Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) Gibco Cat#14175095 Gentle Cell Dissociation Reagent StemCell Technologies Cat#07174 GlutaMAX (100x) Thermo Fisher Scientific Cat#35050–061 Ham’s F12 Medium Cellgro Cat#10–080-CV Iscove’s Modified Dulbecco’s Medium(IMDM) Thermo Fisher Scientific Cat#12440053 N2 Supplement Invitrogen Cat#17502–048 B27 Supplement Invitrogen Cat#15260–037 Primocin Invitrogen Cat#NC9141851 mTeSR1 StemCell Technologies Cat#05850 Open in a separate window KEY RESOURCES TABLE Alveolar progenitor (AT2) cells are transcriptionally distinct upon KRAS expression Alveolar epithelial organoids recapitulate early-stage lung adenocarcinoma Oncogenic KRAS leads to loss of lineage identity in AT2 cells Bulk, scRNAseq, and proteomic data from murine and human KRAS mutant AT2 cells

    Virus:

    Article Title: ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Article Snippet: Cat# 130-106-549 bFGF R&D system Cat# 233-FB-025 Activing A Peprotech Cat# 120-14E-10 Gelatin Millipore Cat# ES-006-B Bovine plasma fibronectin Sigma Cat# F1141 Accutase Sigma Cat# A6964 Nuclei EZ lysis buffer Sigma Cat# N3408 Pierce protease inhibitor, EDTA-free ThermoFisher Cat# A32965 Proteinase K Ambion Cat# AM2546 ProLongTM Gold Antifade Mountant with DAPI ThermoFisher Cat# P36941 Critical Commercial Assays QIAshredder RNA Extraction Column QIAGEN Cat# 79654 RNeasy Plus Mini Kit QIAGEN Cat# 74134 RNase-free DNase set QIAGEN Cat# 79254 miniElute Reaction Cleanup QIAGEN Cat# 28204 TruSeq RNA library kit v2 Illumina Cat# RS-122-2001 Nextera DNA library Prep kit Illumina Cat# FC-121-1031 Nextera Index kit Illumina Cat# FC-121-1012 NEBNext high fidelity 2x PCR master mix NEB Cat# M0541 Ampure XP beads Beckman Coulter Agencourt Cat# A63881 Leukocyte Alkaline Phosphatase kit Sigma Cat# 86R-1KT Deposited Data ATAC-seq ArrayExpress ArrayExpress: E-MTAB-7207 ChIPmentation-seq ArrayExpress ArrayExpress: E-MTAB-7208 RNA-seq ArrayExpress ArrayExpress: E-MTAB-7206 Single cell (sc) RNA-seq ArrayExpress ArrayExpress: E-MTAB-7211 Experimental Models: Cell Lines Mouse Rex1GFPd2 ES cells Yang et al., 2012 N/A (Continued on next page) e1 Cell Reports 27, 3215–3227.e1–e6, June 11, 2019

    Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells
    Article Snippet: 2007 https://matplotlib.org/index.html Seaborn 0.9.0 https://seaborn.pydata.org/# Enrichr in gseapy 0.9.13 Kuleshov et al. 2016 https://github.com/zqfang/GSEApy/blob/master/docs/index.rst Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 van Dijk et al. 2018 https://github.com/KrishnaswamyLab/MAGIC Other ProLongTM Gold Antifade Mountant with DAPI Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"P36935","term_id":"549826","term_text":"P36935"}} P36935 DAPI Sigma-Aldrich Cat#D9542 Transwells Corning Cat#3470 SPRI Select Reagent Beckman Coulter Cat#NC0406407 QubitTM dsDNA HS Assay Kit Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Calcein Blue AM Life Technologies Cat#C1429 Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) Gibco Cat#14175095 Gentle Cell Dissociation Reagent StemCell Technologies Cat#07174 GlutaMAX (100x) Thermo Fisher Scientific Cat#35050–061 Ham’s F12 Medium Cellgro Cat#10–080-CV Iscove’s Modified Dulbecco’s Medium(IMDM) Thermo Fisher Scientific Cat#12440053 N2 Supplement Invitrogen Cat#17502–048 B27 Supplement Invitrogen Cat#15260–037 Primocin Invitrogen Cat#NC9141851 mTeSR1 StemCell Technologies Cat#05850 Open in a separate window KEY RESOURCES TABLE Alveolar progenitor (AT2) cells are transcriptionally distinct upon KRAS expression Alveolar epithelial organoids recapitulate early-stage lung adenocarcinoma Oncogenic KRAS leads to loss of lineage identity in AT2 cells Bulk, scRNAseq, and proteomic data from murine and human KRAS mutant AT2 cells

    Plasmid Preparation:

    Article Title: ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Article Snippet: Cat# 130-106-549 bFGF R&D system Cat# 233-FB-025 Activing A Peprotech Cat# 120-14E-10 Gelatin Millipore Cat# ES-006-B Bovine plasma fibronectin Sigma Cat# F1141 Accutase Sigma Cat# A6964 Nuclei EZ lysis buffer Sigma Cat# N3408 Pierce protease inhibitor, EDTA-free ThermoFisher Cat# A32965 Proteinase K Ambion Cat# AM2546 ProLongTM Gold Antifade Mountant with DAPI ThermoFisher Cat# P36941 Critical Commercial Assays QIAshredder RNA Extraction Column QIAGEN Cat# 79654 RNeasy Plus Mini Kit QIAGEN Cat# 74134 RNase-free DNase set QIAGEN Cat# 79254 miniElute Reaction Cleanup QIAGEN Cat# 28204 TruSeq RNA library kit v2 Illumina Cat# RS-122-2001 Nextera DNA library Prep kit Illumina Cat# FC-121-1031 Nextera Index kit Illumina Cat# FC-121-1012 NEBNext high fidelity 2x PCR master mix NEB Cat# M0541 Ampure XP beads Beckman Coulter Agencourt Cat# A63881 Leukocyte Alkaline Phosphatase kit Sigma Cat# 86R-1KT Deposited Data ATAC-seq ArrayExpress ArrayExpress: E-MTAB-7207 ChIPmentation-seq ArrayExpress ArrayExpress: E-MTAB-7208 RNA-seq ArrayExpress ArrayExpress: E-MTAB-7206 Single cell (sc) RNA-seq ArrayExpress ArrayExpress: E-MTAB-7211 Experimental Models: Cell Lines Mouse Rex1GFPd2 ES cells Yang et al., 2012 N/A (Continued on next page) e1 Cell Reports 27, 3215–3227.e1–e6, June 11, 2019

    Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells
    Article Snippet: 2007 https://matplotlib.org/index.html Seaborn 0.9.0 https://seaborn.pydata.org/# Enrichr in gseapy 0.9.13 Kuleshov et al. 2016 https://github.com/zqfang/GSEApy/blob/master/docs/index.rst Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 van Dijk et al. 2018 https://github.com/KrishnaswamyLab/MAGIC Other ProLongTM Gold Antifade Mountant with DAPI Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"P36935","term_id":"549826","term_text":"P36935"}} P36935 DAPI Sigma-Aldrich Cat#D9542 Transwells Corning Cat#3470 SPRI Select Reagent Beckman Coulter Cat#NC0406407 QubitTM dsDNA HS Assay Kit Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Calcein Blue AM Life Technologies Cat#C1429 Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) Gibco Cat#14175095 Gentle Cell Dissociation Reagent StemCell Technologies Cat#07174 GlutaMAX (100x) Thermo Fisher Scientific Cat#35050–061 Ham’s F12 Medium Cellgro Cat#10–080-CV Iscove’s Modified Dulbecco’s Medium(IMDM) Thermo Fisher Scientific Cat#12440053 N2 Supplement Invitrogen Cat#17502–048 B27 Supplement Invitrogen Cat#15260–037 Primocin Invitrogen Cat#NC9141851 mTeSR1 StemCell Technologies Cat#05850 Open in a separate window KEY RESOURCES TABLE Alveolar progenitor (AT2) cells are transcriptionally distinct upon KRAS expression Alveolar epithelial organoids recapitulate early-stage lung adenocarcinoma Oncogenic KRAS leads to loss of lineage identity in AT2 cells Bulk, scRNAseq, and proteomic data from murine and human KRAS mutant AT2 cells

    Recombinant:

    Article Title: ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Article Snippet: Cat# 130-106-549 bFGF R&D system Cat# 233-FB-025 Activing A Peprotech Cat# 120-14E-10 Gelatin Millipore Cat# ES-006-B Bovine plasma fibronectin Sigma Cat# F1141 Accutase Sigma Cat# A6964 Nuclei EZ lysis buffer Sigma Cat# N3408 Pierce protease inhibitor, EDTA-free ThermoFisher Cat# A32965 Proteinase K Ambion Cat# AM2546 ProLongTM Gold Antifade Mountant with DAPI ThermoFisher Cat# P36941 Critical Commercial Assays QIAshredder RNA Extraction Column QIAGEN Cat# 79654 RNeasy Plus Mini Kit QIAGEN Cat# 74134 RNase-free DNase set QIAGEN Cat# 79254 miniElute Reaction Cleanup QIAGEN Cat# 28204 TruSeq RNA library kit v2 Illumina Cat# RS-122-2001 Nextera DNA library Prep kit Illumina Cat# FC-121-1031 Nextera Index kit Illumina Cat# FC-121-1012 NEBNext high fidelity 2x PCR master mix NEB Cat# M0541 Ampure XP beads Beckman Coulter Agencourt Cat# A63881 Leukocyte Alkaline Phosphatase kit Sigma Cat# 86R-1KT Deposited Data ATAC-seq ArrayExpress ArrayExpress: E-MTAB-7207 ChIPmentation-seq ArrayExpress ArrayExpress: E-MTAB-7208 RNA-seq ArrayExpress ArrayExpress: E-MTAB-7206 Single cell (sc) RNA-seq ArrayExpress ArrayExpress: E-MTAB-7211 Experimental Models: Cell Lines Mouse Rex1GFPd2 ES cells Yang et al., 2012 N/A (Continued on next page) e1 Cell Reports 27, 3215–3227.e1–e6, June 11, 2019

    Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells
    Article Snippet: 2007 https://matplotlib.org/index.html Seaborn 0.9.0 https://seaborn.pydata.org/# Enrichr in gseapy 0.9.13 Kuleshov et al. 2016 https://github.com/zqfang/GSEApy/blob/master/docs/index.rst Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 van Dijk et al. 2018 https://github.com/KrishnaswamyLab/MAGIC Other ProLongTM Gold Antifade Mountant with DAPI Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"P36935","term_id":"549826","term_text":"P36935"}} P36935 DAPI Sigma-Aldrich Cat#D9542 Transwells Corning Cat#3470 SPRI Select Reagent Beckman Coulter Cat#NC0406407 QubitTM dsDNA HS Assay Kit Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Calcein Blue AM Life Technologies Cat#C1429 Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) Gibco Cat#14175095 Gentle Cell Dissociation Reagent StemCell Technologies Cat#07174 GlutaMAX (100x) Thermo Fisher Scientific Cat#35050–061 Ham’s F12 Medium Cellgro Cat#10–080-CV Iscove’s Modified Dulbecco’s Medium(IMDM) Thermo Fisher Scientific Cat#12440053 N2 Supplement Invitrogen Cat#17502–048 B27 Supplement Invitrogen Cat#15260–037 Primocin Invitrogen Cat#NC9141851 mTeSR1 StemCell Technologies Cat#05850 Open in a separate window KEY RESOURCES TABLE Alveolar progenitor (AT2) cells are transcriptionally distinct upon KRAS expression Alveolar epithelial organoids recapitulate early-stage lung adenocarcinoma Oncogenic KRAS leads to loss of lineage identity in AT2 cells Bulk, scRNAseq, and proteomic data from murine and human KRAS mutant AT2 cells

    Multiplex Assay:

    Article Title: ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Article Snippet: Cat# 130-106-549 bFGF R&D system Cat# 233-FB-025 Activing A Peprotech Cat# 120-14E-10 Gelatin Millipore Cat# ES-006-B Bovine plasma fibronectin Sigma Cat# F1141 Accutase Sigma Cat# A6964 Nuclei EZ lysis buffer Sigma Cat# N3408 Pierce protease inhibitor, EDTA-free ThermoFisher Cat# A32965 Proteinase K Ambion Cat# AM2546 ProLongTM Gold Antifade Mountant with DAPI ThermoFisher Cat# P36941 Critical Commercial Assays QIAshredder RNA Extraction Column QIAGEN Cat# 79654 RNeasy Plus Mini Kit QIAGEN Cat# 74134 RNase-free DNase set QIAGEN Cat# 79254 miniElute Reaction Cleanup QIAGEN Cat# 28204 TruSeq RNA library kit v2 Illumina Cat# RS-122-2001 Nextera DNA library Prep kit Illumina Cat# FC-121-1031 Nextera Index kit Illumina Cat# FC-121-1012 NEBNext high fidelity 2x PCR master mix NEB Cat# M0541 Ampure XP beads Beckman Coulter Agencourt Cat# A63881 Leukocyte Alkaline Phosphatase kit Sigma Cat# 86R-1KT Deposited Data ATAC-seq ArrayExpress ArrayExpress: E-MTAB-7207 ChIPmentation-seq ArrayExpress ArrayExpress: E-MTAB-7208 RNA-seq ArrayExpress ArrayExpress: E-MTAB-7206 Single cell (sc) RNA-seq ArrayExpress ArrayExpress: E-MTAB-7211 Experimental Models: Cell Lines Mouse Rex1GFPd2 ES cells Yang et al., 2012 N/A (Continued on next page) e1 Cell Reports 27, 3215–3227.e1–e6, June 11, 2019

    Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells
    Article Snippet: 2007 https://matplotlib.org/index.html Seaborn 0.9.0 https://seaborn.pydata.org/# Enrichr in gseapy 0.9.13 Kuleshov et al. 2016 https://github.com/zqfang/GSEApy/blob/master/docs/index.rst Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 van Dijk et al. 2018 https://github.com/KrishnaswamyLab/MAGIC Other ProLongTM Gold Antifade Mountant with DAPI Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"P36935","term_id":"549826","term_text":"P36935"}} P36935 DAPI Sigma-Aldrich Cat#D9542 Transwells Corning Cat#3470 SPRI Select Reagent Beckman Coulter Cat#NC0406407 QubitTM dsDNA HS Assay Kit Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Calcein Blue AM Life Technologies Cat#C1429 Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) Gibco Cat#14175095 Gentle Cell Dissociation Reagent StemCell Technologies Cat#07174 GlutaMAX (100x) Thermo Fisher Scientific Cat#35050–061 Ham’s F12 Medium Cellgro Cat#10–080-CV Iscove’s Modified Dulbecco’s Medium(IMDM) Thermo Fisher Scientific Cat#12440053 N2 Supplement Invitrogen Cat#17502–048 B27 Supplement Invitrogen Cat#15260–037 Primocin Invitrogen Cat#NC9141851 mTeSR1 StemCell Technologies Cat#05850 Open in a separate window KEY RESOURCES TABLE Alveolar progenitor (AT2) cells are transcriptionally distinct upon KRAS expression Alveolar epithelial organoids recapitulate early-stage lung adenocarcinoma Oncogenic KRAS leads to loss of lineage identity in AT2 cells Bulk, scRNAseq, and proteomic data from murine and human KRAS mutant AT2 cells

    Lysis:

    Article Title: ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Article Snippet: Cat# 130-106-549 bFGF R&D system Cat# 233-FB-025 Activing A Peprotech Cat# 120-14E-10 Gelatin Millipore Cat# ES-006-B Bovine plasma fibronectin Sigma Cat# F1141 Accutase Sigma Cat# A6964 Nuclei EZ lysis buffer Sigma Cat# N3408 Pierce protease inhibitor, EDTA-free ThermoFisher Cat# A32965 Proteinase K Ambion Cat# AM2546 ProLongTM Gold Antifade Mountant with DAPI ThermoFisher Cat# P36941 Critical Commercial Assays QIAshredder RNA Extraction Column QIAGEN Cat# 79654 RNeasy Plus Mini Kit QIAGEN Cat# 74134 RNase-free DNase set QIAGEN Cat# 79254 miniElute Reaction Cleanup QIAGEN Cat# 28204 TruSeq RNA library kit v2 Illumina Cat# RS-122-2001 Nextera DNA library Prep kit Illumina Cat# FC-121-1031 Nextera Index kit Illumina Cat# FC-121-1012 NEBNext high fidelity 2x PCR master mix NEB Cat# M0541 Ampure XP beads Beckman Coulter Agencourt Cat# A63881 Leukocyte Alkaline Phosphatase kit Sigma Cat# 86R-1KT Deposited Data ATAC-seq ArrayExpress ArrayExpress: E-MTAB-7207 ChIPmentation-seq ArrayExpress ArrayExpress: E-MTAB-7208 RNA-seq ArrayExpress ArrayExpress: E-MTAB-7206 Single cell (sc) RNA-seq ArrayExpress ArrayExpress: E-MTAB-7211 Experimental Models: Cell Lines Mouse Rex1GFPd2 ES cells Yang et al., 2012 N/A (Continued on next page) e1 Cell Reports 27, 3215–3227.e1–e6, June 11, 2019

    Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells
    Article Snippet: 2007 https://matplotlib.org/index.html Seaborn 0.9.0 https://seaborn.pydata.org/# Enrichr in gseapy 0.9.13 Kuleshov et al. 2016 https://github.com/zqfang/GSEApy/blob/master/docs/index.rst Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 van Dijk et al. 2018 https://github.com/KrishnaswamyLab/MAGIC Other ProLongTM Gold Antifade Mountant with DAPI Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"P36935","term_id":"549826","term_text":"P36935"}} P36935 DAPI Sigma-Aldrich Cat#D9542 Transwells Corning Cat#3470 SPRI Select Reagent Beckman Coulter Cat#NC0406407 QubitTM dsDNA HS Assay Kit Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Calcein Blue AM Life Technologies Cat#C1429 Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) Gibco Cat#14175095 Gentle Cell Dissociation Reagent StemCell Technologies Cat#07174 GlutaMAX (100x) Thermo Fisher Scientific Cat#35050–061 Ham’s F12 Medium Cellgro Cat#10–080-CV Iscove’s Modified Dulbecco’s Medium(IMDM) Thermo Fisher Scientific Cat#12440053 N2 Supplement Invitrogen Cat#17502–048 B27 Supplement Invitrogen Cat#15260–037 Primocin Invitrogen Cat#NC9141851 mTeSR1 StemCell Technologies Cat#05850 Open in a separate window KEY RESOURCES TABLE Alveolar progenitor (AT2) cells are transcriptionally distinct upon KRAS expression Alveolar epithelial organoids recapitulate early-stage lung adenocarcinoma Oncogenic KRAS leads to loss of lineage identity in AT2 cells Bulk, scRNAseq, and proteomic data from murine and human KRAS mutant AT2 cells

    Reverse Transcription:

    Article Title: ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Article Snippet: Cat# 130-106-549 bFGF R&D system Cat# 233-FB-025 Activing A Peprotech Cat# 120-14E-10 Gelatin Millipore Cat# ES-006-B Bovine plasma fibronectin Sigma Cat# F1141 Accutase Sigma Cat# A6964 Nuclei EZ lysis buffer Sigma Cat# N3408 Pierce protease inhibitor, EDTA-free ThermoFisher Cat# A32965 Proteinase K Ambion Cat# AM2546 ProLongTM Gold Antifade Mountant with DAPI ThermoFisher Cat# P36941 Critical Commercial Assays QIAshredder RNA Extraction Column QIAGEN Cat# 79654 RNeasy Plus Mini Kit QIAGEN Cat# 74134 RNase-free DNase set QIAGEN Cat# 79254 miniElute Reaction Cleanup QIAGEN Cat# 28204 TruSeq RNA library kit v2 Illumina Cat# RS-122-2001 Nextera DNA library Prep kit Illumina Cat# FC-121-1031 Nextera Index kit Illumina Cat# FC-121-1012 NEBNext high fidelity 2x PCR master mix NEB Cat# M0541 Ampure XP beads Beckman Coulter Agencourt Cat# A63881 Leukocyte Alkaline Phosphatase kit Sigma Cat# 86R-1KT Deposited Data ATAC-seq ArrayExpress ArrayExpress: E-MTAB-7207 ChIPmentation-seq ArrayExpress ArrayExpress: E-MTAB-7208 RNA-seq ArrayExpress ArrayExpress: E-MTAB-7206 Single cell (sc) RNA-seq ArrayExpress ArrayExpress: E-MTAB-7211 Experimental Models: Cell Lines Mouse Rex1GFPd2 ES cells Yang et al., 2012 N/A (Continued on next page) e1 Cell Reports 27, 3215–3227.e1–e6, June 11, 2019

    Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells
    Article Snippet: 2007 https://matplotlib.org/index.html Seaborn 0.9.0 https://seaborn.pydata.org/# Enrichr in gseapy 0.9.13 Kuleshov et al. 2016 https://github.com/zqfang/GSEApy/blob/master/docs/index.rst Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 van Dijk et al. 2018 https://github.com/KrishnaswamyLab/MAGIC Other ProLongTM Gold Antifade Mountant with DAPI Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"P36935","term_id":"549826","term_text":"P36935"}} P36935 DAPI Sigma-Aldrich Cat#D9542 Transwells Corning Cat#3470 SPRI Select Reagent Beckman Coulter Cat#NC0406407 QubitTM dsDNA HS Assay Kit Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Calcein Blue AM Life Technologies Cat#C1429 Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) Gibco Cat#14175095 Gentle Cell Dissociation Reagent StemCell Technologies Cat#07174 GlutaMAX (100x) Thermo Fisher Scientific Cat#35050–061 Ham’s F12 Medium Cellgro Cat#10–080-CV Iscove’s Modified Dulbecco’s Medium(IMDM) Thermo Fisher Scientific Cat#12440053 N2 Supplement Invitrogen Cat#17502–048 B27 Supplement Invitrogen Cat#15260–037 Primocin Invitrogen Cat#NC9141851 mTeSR1 StemCell Technologies Cat#05850 Open in a separate window KEY RESOURCES TABLE Alveolar progenitor (AT2) cells are transcriptionally distinct upon KRAS expression Alveolar epithelial organoids recapitulate early-stage lung adenocarcinoma Oncogenic KRAS leads to loss of lineage identity in AT2 cells Bulk, scRNAseq, and proteomic data from murine and human KRAS mutant AT2 cells

    Mass Spectrometry:

    Article Title: ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Article Snippet: Cat# 130-106-549 bFGF R&D system Cat# 233-FB-025 Activing A Peprotech Cat# 120-14E-10 Gelatin Millipore Cat# ES-006-B Bovine plasma fibronectin Sigma Cat# F1141 Accutase Sigma Cat# A6964 Nuclei EZ lysis buffer Sigma Cat# N3408 Pierce protease inhibitor, EDTA-free ThermoFisher Cat# A32965 Proteinase K Ambion Cat# AM2546 ProLongTM Gold Antifade Mountant with DAPI ThermoFisher Cat# P36941 Critical Commercial Assays QIAshredder RNA Extraction Column QIAGEN Cat# 79654 RNeasy Plus Mini Kit QIAGEN Cat# 74134 RNase-free DNase set QIAGEN Cat# 79254 miniElute Reaction Cleanup QIAGEN Cat# 28204 TruSeq RNA library kit v2 Illumina Cat# RS-122-2001 Nextera DNA library Prep kit Illumina Cat# FC-121-1031 Nextera Index kit Illumina Cat# FC-121-1012 NEBNext high fidelity 2x PCR master mix NEB Cat# M0541 Ampure XP beads Beckman Coulter Agencourt Cat# A63881 Leukocyte Alkaline Phosphatase kit Sigma Cat# 86R-1KT Deposited Data ATAC-seq ArrayExpress ArrayExpress: E-MTAB-7207 ChIPmentation-seq ArrayExpress ArrayExpress: E-MTAB-7208 RNA-seq ArrayExpress ArrayExpress: E-MTAB-7206 Single cell (sc) RNA-seq ArrayExpress ArrayExpress: E-MTAB-7211 Experimental Models: Cell Lines Mouse Rex1GFPd2 ES cells Yang et al., 2012 N/A (Continued on next page) e1 Cell Reports 27, 3215–3227.e1–e6, June 11, 2019

    Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells
    Article Snippet: 2007 https://matplotlib.org/index.html Seaborn 0.9.0 https://seaborn.pydata.org/# Enrichr in gseapy 0.9.13 Kuleshov et al. 2016 https://github.com/zqfang/GSEApy/blob/master/docs/index.rst Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 van Dijk et al. 2018 https://github.com/KrishnaswamyLab/MAGIC Other ProLongTM Gold Antifade Mountant with DAPI Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"P36935","term_id":"549826","term_text":"P36935"}} P36935 DAPI Sigma-Aldrich Cat#D9542 Transwells Corning Cat#3470 SPRI Select Reagent Beckman Coulter Cat#NC0406407 QubitTM dsDNA HS Assay Kit Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Calcein Blue AM Life Technologies Cat#C1429 Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) Gibco Cat#14175095 Gentle Cell Dissociation Reagent StemCell Technologies Cat#07174 GlutaMAX (100x) Thermo Fisher Scientific Cat#35050–061 Ham’s F12 Medium Cellgro Cat#10–080-CV Iscove’s Modified Dulbecco’s Medium(IMDM) Thermo Fisher Scientific Cat#12440053 N2 Supplement Invitrogen Cat#17502–048 B27 Supplement Invitrogen Cat#15260–037 Primocin Invitrogen Cat#NC9141851 mTeSR1 StemCell Technologies Cat#05850 Open in a separate window KEY RESOURCES TABLE Alveolar progenitor (AT2) cells are transcriptionally distinct upon KRAS expression Alveolar epithelial organoids recapitulate early-stage lung adenocarcinoma Oncogenic KRAS leads to loss of lineage identity in AT2 cells Bulk, scRNAseq, and proteomic data from murine and human KRAS mutant AT2 cells

    Gene Expression:

    Article Title: ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Article Snippet: Cat# 130-106-549 bFGF R&D system Cat# 233-FB-025 Activing A Peprotech Cat# 120-14E-10 Gelatin Millipore Cat# ES-006-B Bovine plasma fibronectin Sigma Cat# F1141 Accutase Sigma Cat# A6964 Nuclei EZ lysis buffer Sigma Cat# N3408 Pierce protease inhibitor, EDTA-free ThermoFisher Cat# A32965 Proteinase K Ambion Cat# AM2546 ProLongTM Gold Antifade Mountant with DAPI ThermoFisher Cat# P36941 Critical Commercial Assays QIAshredder RNA Extraction Column QIAGEN Cat# 79654 RNeasy Plus Mini Kit QIAGEN Cat# 74134 RNase-free DNase set QIAGEN Cat# 79254 miniElute Reaction Cleanup QIAGEN Cat# 28204 TruSeq RNA library kit v2 Illumina Cat# RS-122-2001 Nextera DNA library Prep kit Illumina Cat# FC-121-1031 Nextera Index kit Illumina Cat# FC-121-1012 NEBNext high fidelity 2x PCR master mix NEB Cat# M0541 Ampure XP beads Beckman Coulter Agencourt Cat# A63881 Leukocyte Alkaline Phosphatase kit Sigma Cat# 86R-1KT Deposited Data ATAC-seq ArrayExpress ArrayExpress: E-MTAB-7207 ChIPmentation-seq ArrayExpress ArrayExpress: E-MTAB-7208 RNA-seq ArrayExpress ArrayExpress: E-MTAB-7206 Single cell (sc) RNA-seq ArrayExpress ArrayExpress: E-MTAB-7211 Experimental Models: Cell Lines Mouse Rex1GFPd2 ES cells Yang et al., 2012 N/A (Continued on next page) e1 Cell Reports 27, 3215–3227.e1–e6, June 11, 2019

    Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells
    Article Snippet: 2007 https://matplotlib.org/index.html Seaborn 0.9.0 https://seaborn.pydata.org/# Enrichr in gseapy 0.9.13 Kuleshov et al. 2016 https://github.com/zqfang/GSEApy/blob/master/docs/index.rst Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 van Dijk et al. 2018 https://github.com/KrishnaswamyLab/MAGIC Other ProLongTM Gold Antifade Mountant with DAPI Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"P36935","term_id":"549826","term_text":"P36935"}} P36935 DAPI Sigma-Aldrich Cat#D9542 Transwells Corning Cat#3470 SPRI Select Reagent Beckman Coulter Cat#NC0406407 QubitTM dsDNA HS Assay Kit Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Calcein Blue AM Life Technologies Cat#C1429 Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) Gibco Cat#14175095 Gentle Cell Dissociation Reagent StemCell Technologies Cat#07174 GlutaMAX (100x) Thermo Fisher Scientific Cat#35050–061 Ham’s F12 Medium Cellgro Cat#10–080-CV Iscove’s Modified Dulbecco’s Medium(IMDM) Thermo Fisher Scientific Cat#12440053 N2 Supplement Invitrogen Cat#17502–048 B27 Supplement Invitrogen Cat#15260–037 Primocin Invitrogen Cat#NC9141851 mTeSR1 StemCell Technologies Cat#05850 Open in a separate window KEY RESOURCES TABLE Alveolar progenitor (AT2) cells are transcriptionally distinct upon KRAS expression Alveolar epithelial organoids recapitulate early-stage lung adenocarcinoma Oncogenic KRAS leads to loss of lineage identity in AT2 cells Bulk, scRNAseq, and proteomic data from murine and human KRAS mutant AT2 cells

    Software:

    Article Title: ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Article Snippet: Cat# 130-106-549 bFGF R&D system Cat# 233-FB-025 Activing A Peprotech Cat# 120-14E-10 Gelatin Millipore Cat# ES-006-B Bovine plasma fibronectin Sigma Cat# F1141 Accutase Sigma Cat# A6964 Nuclei EZ lysis buffer Sigma Cat# N3408 Pierce protease inhibitor, EDTA-free ThermoFisher Cat# A32965 Proteinase K Ambion Cat# AM2546 ProLongTM Gold Antifade Mountant with DAPI ThermoFisher Cat# P36941 Critical Commercial Assays QIAshredder RNA Extraction Column QIAGEN Cat# 79654 RNeasy Plus Mini Kit QIAGEN Cat# 74134 RNase-free DNase set QIAGEN Cat# 79254 miniElute Reaction Cleanup QIAGEN Cat# 28204 TruSeq RNA library kit v2 Illumina Cat# RS-122-2001 Nextera DNA library Prep kit Illumina Cat# FC-121-1031 Nextera Index kit Illumina Cat# FC-121-1012 NEBNext high fidelity 2x PCR master mix NEB Cat# M0541 Ampure XP beads Beckman Coulter Agencourt Cat# A63881 Leukocyte Alkaline Phosphatase kit Sigma Cat# 86R-1KT Deposited Data ATAC-seq ArrayExpress ArrayExpress: E-MTAB-7207 ChIPmentation-seq ArrayExpress ArrayExpress: E-MTAB-7208 RNA-seq ArrayExpress ArrayExpress: E-MTAB-7206 Single cell (sc) RNA-seq ArrayExpress ArrayExpress: E-MTAB-7211 Experimental Models: Cell Lines Mouse Rex1GFPd2 ES cells Yang et al., 2012 N/A (Continued on next page) e1 Cell Reports 27, 3215–3227.e1–e6, June 11, 2019

    Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells
    Article Snippet: 2007 https://matplotlib.org/index.html Seaborn 0.9.0 https://seaborn.pydata.org/# Enrichr in gseapy 0.9.13 Kuleshov et al. 2016 https://github.com/zqfang/GSEApy/blob/master/docs/index.rst Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 van Dijk et al. 2018 https://github.com/KrishnaswamyLab/MAGIC Other ProLongTM Gold Antifade Mountant with DAPI Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"P36935","term_id":"549826","term_text":"P36935"}} P36935 DAPI Sigma-Aldrich Cat#D9542 Transwells Corning Cat#3470 SPRI Select Reagent Beckman Coulter Cat#NC0406407 QubitTM dsDNA HS Assay Kit Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Calcein Blue AM Life Technologies Cat#C1429 Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) Gibco Cat#14175095 Gentle Cell Dissociation Reagent StemCell Technologies Cat#07174 GlutaMAX (100x) Thermo Fisher Scientific Cat#35050–061 Ham’s F12 Medium Cellgro Cat#10–080-CV Iscove’s Modified Dulbecco’s Medium(IMDM) Thermo Fisher Scientific Cat#12440053 N2 Supplement Invitrogen Cat#17502–048 B27 Supplement Invitrogen Cat#15260–037 Primocin Invitrogen Cat#NC9141851 mTeSR1 StemCell Technologies Cat#05850 Open in a separate window KEY RESOURCES TABLE Alveolar progenitor (AT2) cells are transcriptionally distinct upon KRAS expression Alveolar epithelial organoids recapitulate early-stage lung adenocarcinoma Oncogenic KRAS leads to loss of lineage identity in AT2 cells Bulk, scRNAseq, and proteomic data from murine and human KRAS mutant AT2 cells

    Clinical Proteomics:

    Article Title: ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Article Snippet: Cat# 130-106-549 bFGF R&D system Cat# 233-FB-025 Activing A Peprotech Cat# 120-14E-10 Gelatin Millipore Cat# ES-006-B Bovine plasma fibronectin Sigma Cat# F1141 Accutase Sigma Cat# A6964 Nuclei EZ lysis buffer Sigma Cat# N3408 Pierce protease inhibitor, EDTA-free ThermoFisher Cat# A32965 Proteinase K Ambion Cat# AM2546 ProLongTM Gold Antifade Mountant with DAPI ThermoFisher Cat# P36941 Critical Commercial Assays QIAshredder RNA Extraction Column QIAGEN Cat# 79654 RNeasy Plus Mini Kit QIAGEN Cat# 74134 RNase-free DNase set QIAGEN Cat# 79254 miniElute Reaction Cleanup QIAGEN Cat# 28204 TruSeq RNA library kit v2 Illumina Cat# RS-122-2001 Nextera DNA library Prep kit Illumina Cat# FC-121-1031 Nextera Index kit Illumina Cat# FC-121-1012 NEBNext high fidelity 2x PCR master mix NEB Cat# M0541 Ampure XP beads Beckman Coulter Agencourt Cat# A63881 Leukocyte Alkaline Phosphatase kit Sigma Cat# 86R-1KT Deposited Data ATAC-seq ArrayExpress ArrayExpress: E-MTAB-7207 ChIPmentation-seq ArrayExpress ArrayExpress: E-MTAB-7208 RNA-seq ArrayExpress ArrayExpress: E-MTAB-7206 Single cell (sc) RNA-seq ArrayExpress ArrayExpress: E-MTAB-7211 Experimental Models: Cell Lines Mouse Rex1GFPd2 ES cells Yang et al., 2012 N/A (Continued on next page) e1 Cell Reports 27, 3215–3227.e1–e6, June 11, 2019

    Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells
    Article Snippet: 2007 https://matplotlib.org/index.html Seaborn 0.9.0 https://seaborn.pydata.org/# Enrichr in gseapy 0.9.13 Kuleshov et al. 2016 https://github.com/zqfang/GSEApy/blob/master/docs/index.rst Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 van Dijk et al. 2018 https://github.com/KrishnaswamyLab/MAGIC Other ProLongTM Gold Antifade Mountant with DAPI Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"P36935","term_id":"549826","term_text":"P36935"}} P36935 DAPI Sigma-Aldrich Cat#D9542 Transwells Corning Cat#3470 SPRI Select Reagent Beckman Coulter Cat#NC0406407 QubitTM dsDNA HS Assay Kit Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Calcein Blue AM Life Technologies Cat#C1429 Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) Gibco Cat#14175095 Gentle Cell Dissociation Reagent StemCell Technologies Cat#07174 GlutaMAX (100x) Thermo Fisher Scientific Cat#35050–061 Ham’s F12 Medium Cellgro Cat#10–080-CV Iscove’s Modified Dulbecco’s Medium(IMDM) Thermo Fisher Scientific Cat#12440053 N2 Supplement Invitrogen Cat#17502–048 B27 Supplement Invitrogen Cat#15260–037 Primocin Invitrogen Cat#NC9141851 mTeSR1 StemCell Technologies Cat#05850 Open in a separate window KEY RESOURCES TABLE Alveolar progenitor (AT2) cells are transcriptionally distinct upon KRAS expression Alveolar epithelial organoids recapitulate early-stage lung adenocarcinoma Oncogenic KRAS leads to loss of lineage identity in AT2 cells Bulk, scRNAseq, and proteomic data from murine and human KRAS mutant AT2 cells

    Protease Inhibitor:

    Article Title: ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Article Snippet: Cat# 130-106-549 bFGF R&D system Cat# 233-FB-025 Activing A Peprotech Cat# 120-14E-10 Gelatin Millipore Cat# ES-006-B Bovine plasma fibronectin Sigma Cat# F1141 Accutase Sigma Cat# A6964 Nuclei EZ lysis buffer Sigma Cat# N3408 Pierce protease inhibitor, EDTA-free ThermoFisher Cat# A32965 Proteinase K Ambion Cat# AM2546 ProLongTM Gold Antifade Mountant with DAPI ThermoFisher Cat# P36941 Critical Commercial Assays QIAshredder RNA Extraction Column QIAGEN Cat# 79654 RNeasy Plus Mini Kit QIAGEN Cat# 74134 RNase-free DNase set QIAGEN Cat# 79254 miniElute Reaction Cleanup QIAGEN Cat# 28204 TruSeq RNA library kit v2 Illumina Cat# RS-122-2001 Nextera DNA library Prep kit Illumina Cat# FC-121-1031 Nextera Index kit Illumina Cat# FC-121-1012 NEBNext high fidelity 2x PCR master mix NEB Cat# M0541 Ampure XP beads Beckman Coulter Agencourt Cat# A63881 Leukocyte Alkaline Phosphatase kit Sigma Cat# 86R-1KT Deposited Data ATAC-seq ArrayExpress ArrayExpress: E-MTAB-7207 ChIPmentation-seq ArrayExpress ArrayExpress: E-MTAB-7208 RNA-seq ArrayExpress ArrayExpress: E-MTAB-7206 Single cell (sc) RNA-seq ArrayExpress ArrayExpress: E-MTAB-7211 Experimental Models: Cell Lines Mouse Rex1GFPd2 ES cells Yang et al., 2012 N/A (Continued on next page) e1 Cell Reports 27, 3215–3227.e1–e6, June 11, 2019

    Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells
    Article Snippet: 2007 https://matplotlib.org/index.html Seaborn 0.9.0 https://seaborn.pydata.org/# Enrichr in gseapy 0.9.13 Kuleshov et al. 2016 https://github.com/zqfang/GSEApy/blob/master/docs/index.rst Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 van Dijk et al. 2018 https://github.com/KrishnaswamyLab/MAGIC Other ProLongTM Gold Antifade Mountant with DAPI Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"P36935","term_id":"549826","term_text":"P36935"}} P36935 DAPI Sigma-Aldrich Cat#D9542 Transwells Corning Cat#3470 SPRI Select Reagent Beckman Coulter Cat#NC0406407 QubitTM dsDNA HS Assay Kit Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Calcein Blue AM Life Technologies Cat#C1429 Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) Gibco Cat#14175095 Gentle Cell Dissociation Reagent StemCell Technologies Cat#07174 GlutaMAX (100x) Thermo Fisher Scientific Cat#35050–061 Ham’s F12 Medium Cellgro Cat#10–080-CV Iscove’s Modified Dulbecco’s Medium(IMDM) Thermo Fisher Scientific Cat#12440053 N2 Supplement Invitrogen Cat#17502–048 B27 Supplement Invitrogen Cat#15260–037 Primocin Invitrogen Cat#NC9141851 mTeSR1 StemCell Technologies Cat#05850 Open in a separate window KEY RESOURCES TABLE Alveolar progenitor (AT2) cells are transcriptionally distinct upon KRAS expression Alveolar epithelial organoids recapitulate early-stage lung adenocarcinoma Oncogenic KRAS leads to loss of lineage identity in AT2 cells Bulk, scRNAseq, and proteomic data from murine and human KRAS mutant AT2 cells

    RNA Extraction:

    Article Title: ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Article Snippet: Cat# 130-106-549 bFGF R&D system Cat# 233-FB-025 Activing A Peprotech Cat# 120-14E-10 Gelatin Millipore Cat# ES-006-B Bovine plasma fibronectin Sigma Cat# F1141 Accutase Sigma Cat# A6964 Nuclei EZ lysis buffer Sigma Cat# N3408 Pierce protease inhibitor, EDTA-free ThermoFisher Cat# A32965 Proteinase K Ambion Cat# AM2546 ProLongTM Gold Antifade Mountant with DAPI ThermoFisher Cat# P36941 Critical Commercial Assays QIAshredder RNA Extraction Column QIAGEN Cat# 79654 RNeasy Plus Mini Kit QIAGEN Cat# 74134 RNase-free DNase set QIAGEN Cat# 79254 miniElute Reaction Cleanup QIAGEN Cat# 28204 TruSeq RNA library kit v2 Illumina Cat# RS-122-2001 Nextera DNA library Prep kit Illumina Cat# FC-121-1031 Nextera Index kit Illumina Cat# FC-121-1012 NEBNext high fidelity 2x PCR master mix NEB Cat# M0541 Ampure XP beads Beckman Coulter Agencourt Cat# A63881 Leukocyte Alkaline Phosphatase kit Sigma Cat# 86R-1KT Deposited Data ATAC-seq ArrayExpress ArrayExpress: E-MTAB-7207 ChIPmentation-seq ArrayExpress ArrayExpress: E-MTAB-7208 RNA-seq ArrayExpress ArrayExpress: E-MTAB-7206 Single cell (sc) RNA-seq ArrayExpress ArrayExpress: E-MTAB-7211 Experimental Models: Cell Lines Mouse Rex1GFPd2 ES cells Yang et al., 2012 N/A (Continued on next page) e1 Cell Reports 27, 3215–3227.e1–e6, June 11, 2019

    Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells
    Article Snippet: 2007 https://matplotlib.org/index.html Seaborn 0.9.0 https://seaborn.pydata.org/# Enrichr in gseapy 0.9.13 Kuleshov et al. 2016 https://github.com/zqfang/GSEApy/blob/master/docs/index.rst Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 van Dijk et al. 2018 https://github.com/KrishnaswamyLab/MAGIC Other ProLongTM Gold Antifade Mountant with DAPI Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"P36935","term_id":"549826","term_text":"P36935"}} P36935 DAPI Sigma-Aldrich Cat#D9542 Transwells Corning Cat#3470 SPRI Select Reagent Beckman Coulter Cat#NC0406407 QubitTM dsDNA HS Assay Kit Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Calcein Blue AM Life Technologies Cat#C1429 Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) Gibco Cat#14175095 Gentle Cell Dissociation Reagent StemCell Technologies Cat#07174 GlutaMAX (100x) Thermo Fisher Scientific Cat#35050–061 Ham’s F12 Medium Cellgro Cat#10–080-CV Iscove’s Modified Dulbecco’s Medium(IMDM) Thermo Fisher Scientific Cat#12440053 N2 Supplement Invitrogen Cat#17502–048 B27 Supplement Invitrogen Cat#15260–037 Primocin Invitrogen Cat#NC9141851 mTeSR1 StemCell Technologies Cat#05850 Open in a separate window KEY RESOURCES TABLE Alveolar progenitor (AT2) cells are transcriptionally distinct upon KRAS expression Alveolar epithelial organoids recapitulate early-stage lung adenocarcinoma Oncogenic KRAS leads to loss of lineage identity in AT2 cells Bulk, scRNAseq, and proteomic data from murine and human KRAS mutant AT2 cells

    Polymerase Chain Reaction:

    Article Title: ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Article Snippet: Cat# 130-106-549 bFGF R&D system Cat# 233-FB-025 Activing A Peprotech Cat# 120-14E-10 Gelatin Millipore Cat# ES-006-B Bovine plasma fibronectin Sigma Cat# F1141 Accutase Sigma Cat# A6964 Nuclei EZ lysis buffer Sigma Cat# N3408 Pierce protease inhibitor, EDTA-free ThermoFisher Cat# A32965 Proteinase K Ambion Cat# AM2546 ProLongTM Gold Antifade Mountant with DAPI ThermoFisher Cat# P36941 Critical Commercial Assays QIAshredder RNA Extraction Column QIAGEN Cat# 79654 RNeasy Plus Mini Kit QIAGEN Cat# 74134 RNase-free DNase set QIAGEN Cat# 79254 miniElute Reaction Cleanup QIAGEN Cat# 28204 TruSeq RNA library kit v2 Illumina Cat# RS-122-2001 Nextera DNA library Prep kit Illumina Cat# FC-121-1031 Nextera Index kit Illumina Cat# FC-121-1012 NEBNext high fidelity 2x PCR master mix NEB Cat# M0541 Ampure XP beads Beckman Coulter Agencourt Cat# A63881 Leukocyte Alkaline Phosphatase kit Sigma Cat# 86R-1KT Deposited Data ATAC-seq ArrayExpress ArrayExpress: E-MTAB-7207 ChIPmentation-seq ArrayExpress ArrayExpress: E-MTAB-7208 RNA-seq ArrayExpress ArrayExpress: E-MTAB-7206 Single cell (sc) RNA-seq ArrayExpress ArrayExpress: E-MTAB-7211 Experimental Models: Cell Lines Mouse Rex1GFPd2 ES cells Yang et al., 2012 N/A (Continued on next page) e1 Cell Reports 27, 3215–3227.e1–e6, June 11, 2019

    Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells
    Article Snippet: 2007 https://matplotlib.org/index.html Seaborn 0.9.0 https://seaborn.pydata.org/# Enrichr in gseapy 0.9.13 Kuleshov et al. 2016 https://github.com/zqfang/GSEApy/blob/master/docs/index.rst Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 van Dijk et al. 2018 https://github.com/KrishnaswamyLab/MAGIC Other ProLongTM Gold Antifade Mountant with DAPI Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"P36935","term_id":"549826","term_text":"P36935"}} P36935 DAPI Sigma-Aldrich Cat#D9542 Transwells Corning Cat#3470 SPRI Select Reagent Beckman Coulter Cat#NC0406407 QubitTM dsDNA HS Assay Kit Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Calcein Blue AM Life Technologies Cat#C1429 Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) Gibco Cat#14175095 Gentle Cell Dissociation Reagent StemCell Technologies Cat#07174 GlutaMAX (100x) Thermo Fisher Scientific Cat#35050–061 Ham’s F12 Medium Cellgro Cat#10–080-CV Iscove’s Modified Dulbecco’s Medium(IMDM) Thermo Fisher Scientific Cat#12440053 N2 Supplement Invitrogen Cat#17502–048 B27 Supplement Invitrogen Cat#15260–037 Primocin Invitrogen Cat#NC9141851 mTeSR1 StemCell Technologies Cat#05850 Open in a separate window KEY RESOURCES TABLE Alveolar progenitor (AT2) cells are transcriptionally distinct upon KRAS expression Alveolar epithelial organoids recapitulate early-stage lung adenocarcinoma Oncogenic KRAS leads to loss of lineage identity in AT2 cells Bulk, scRNAseq, and proteomic data from murine and human KRAS mutant AT2 cells

    RNA Sequencing:

    Article Title: ZIC3 Controls the Transition from Naive to Primed Pluripotency
    Article Snippet: Cat# 130-106-549 bFGF R&D system Cat# 233-FB-025 Activing A Peprotech Cat# 120-14E-10 Gelatin Millipore Cat# ES-006-B Bovine plasma fibronectin Sigma Cat# F1141 Accutase Sigma Cat# A6964 Nuclei EZ lysis buffer Sigma Cat# N3408 Pierce protease inhibitor, EDTA-free ThermoFisher Cat# A32965 Proteinase K Ambion Cat# AM2546 ProLongTM Gold Antifade Mountant with DAPI ThermoFisher Cat# P36941 Critical Commercial Assays QIAshredder RNA Extraction Column QIAGEN Cat# 79654 RNeasy Plus Mini Kit QIAGEN Cat# 74134 RNase-free DNase set QIAGEN Cat# 79254 miniElute Reaction Cleanup QIAGEN Cat# 28204 TruSeq RNA library kit v2 Illumina Cat# RS-122-2001 Nextera DNA library Prep kit Illumina Cat# FC-121-1031 Nextera Index kit Illumina Cat# FC-121-1012 NEBNext high fidelity 2x PCR master mix NEB Cat# M0541 Ampure XP beads Beckman Coulter Agencourt Cat# A63881 Leukocyte Alkaline Phosphatase kit Sigma Cat# 86R-1KT Deposited Data ATAC-seq ArrayExpress ArrayExpress: E-MTAB-7207 ChIPmentation-seq ArrayExpress ArrayExpress: E-MTAB-7208 RNA-seq ArrayExpress ArrayExpress: E-MTAB-7206 Single cell (sc) RNA-seq ArrayExpress ArrayExpress: E-MTAB-7211 Experimental Models: Cell Lines Mouse Rex1GFPd2 ES cells Yang et al., 2012 N/A (Continued on next page) e1 Cell Reports 27, 3215–3227.e1–e6, June 11, 2019

    Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells
    Article Snippet: 2007 https://matplotlib.org/index.html Seaborn 0.9.0 https://seaborn.pydata.org/# Enrichr in gseapy 0.9.13 Kuleshov et al. 2016 https://github.com/zqfang/GSEApy/blob/master/docs/index.rst Markov Affinity-based Graph Imputation of Cells (MAGIC) 1.5.5 van Dijk et al. 2018 https://github.com/KrishnaswamyLab/MAGIC Other ProLongTM Gold Antifade Mountant with DAPI Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"P36935","term_id":"549826","term_text":"P36935"}} P36935 DAPI Sigma-Aldrich Cat#D9542 Transwells Corning Cat#3470 SPRI Select Reagent Beckman Coulter Cat#NC0406407 QubitTM dsDNA HS Assay Kit Invitrogen Cat# {"type":"entrez-protein","attrs":{"text":"Q32851","term_id":"75280859","term_text":"Q32851"}} Q32851 Calcein Blue AM Life Technologies Cat#C1429 Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) Gibco Cat#14175095 Gentle Cell Dissociation Reagent StemCell Technologies Cat#07174 GlutaMAX (100x) Thermo Fisher Scientific Cat#35050–061 Ham’s F12 Medium Cellgro Cat#10–080-CV Iscove’s Modified Dulbecco’s Medium(IMDM) Thermo Fisher Scientific Cat#12440053 N2 Supplement Invitrogen Cat#17502–048 B27 Supplement Invitrogen Cat#15260–037 Primocin Invitrogen Cat#NC9141851 mTeSR1 StemCell Technologies Cat#05850 Open in a separate window KEY RESOURCES TABLE Alveolar progenitor (AT2) cells are transcriptionally distinct upon KRAS expression Alveolar epithelial organoids recapitulate early-stage lung adenocarcinoma Oncogenic KRAS leads to loss of lineage identity in AT2 cells Bulk, scRNAseq, and proteomic data from murine and human KRAS mutant AT2 cells



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    Image Search Results


    Expression and immunolocalization of histamine H3 receptor (H3R) in the cochlea of P4-5 C57BL/6 mice. a Relative H3R mRNA expression in the organ of Corti (OC), lateral wall (LW), and modiolus (MOD). Each sample consisted of tissue from four mice, with three biological replicates per group. b Schematic illustration of a mid-modiolar section of the mouse cochlea highlighting major anatomical structures within the scala media. Reproduced with permission obtained from Springer Nature under CC BY 4.0 . c Low-magnification image of a longitudinal cochlear cryosection. d – e High-magnification views of the boxed regions in c. f Immunofluorescence staining showing co-localization of H3R and phalloidin in both inner and outer HCs within the organ of Corti. H3R (green in c-e, red in f), Phalloidin (green in f), nuclei (DAPI, blue). Scale bars: 200 μm in c , 100 μm in d-e , 10 μm in f

    Journal: Neurochemical Research

    Article Title: Histamine H3 Receptor Antagonists Influence the Directional Growth of Type II Spiral Ganglion Neurites Within the Developing Cochlea of C57BL/6 Mice

    doi: 10.1007/s11064-025-04521-9

    Figure Lengend Snippet: Expression and immunolocalization of histamine H3 receptor (H3R) in the cochlea of P4-5 C57BL/6 mice. a Relative H3R mRNA expression in the organ of Corti (OC), lateral wall (LW), and modiolus (MOD). Each sample consisted of tissue from four mice, with three biological replicates per group. b Schematic illustration of a mid-modiolar section of the mouse cochlea highlighting major anatomical structures within the scala media. Reproduced with permission obtained from Springer Nature under CC BY 4.0 . c Low-magnification image of a longitudinal cochlear cryosection. d – e High-magnification views of the boxed regions in c. f Immunofluorescence staining showing co-localization of H3R and phalloidin in both inner and outer HCs within the organ of Corti. H3R (green in c-e, red in f), Phalloidin (green in f), nuclei (DAPI, blue). Scale bars: 200 μm in c , 100 μm in d-e , 10 μm in f

    Article Snippet: Nuclear staining was performed using ProLong Gold Antifade Mountant with DAPI (cat. #8961S, Cell Signaling Technology, USA).

    Techniques: Expressing, Immunofluorescence, Staining

    Localization of H3R in hair cells (HCs) and spiral ganglion neurons (SGNs), and its absence at ribbon synapses. a Immunofluorescence staining showing H3R expression in both inner and outer HCs within the organ of Corti. b Negative control incubated only with the secondary antibody (Alexa Fluor™ 488) without the primary anti-H3R antibody. c High-magnification image illustrating H3R signals at the neurite terminals of SGNs near the HCs. d – e Representative images demonstrating H3R expression in SGNs and the corresponding negative control. f High-magnification image showing H3R localization in both the somata and neurites of SGNs. g – i No colocalization is observed between Ribeye and H3R, indicating the absence of H3R at ribbon synapses. H3R (green); neurofilament 200 (NF200, red in a–f); Ribeye (red in g–i); nuclei (DAPI, blue). Scale bars: 15 μm in a – c ; 20 μm in d , e , g ; 5 μm in f ; 10 μm in h , i

    Journal: Neurochemical Research

    Article Title: Histamine H3 Receptor Antagonists Influence the Directional Growth of Type II Spiral Ganglion Neurites Within the Developing Cochlea of C57BL/6 Mice

    doi: 10.1007/s11064-025-04521-9

    Figure Lengend Snippet: Localization of H3R in hair cells (HCs) and spiral ganglion neurons (SGNs), and its absence at ribbon synapses. a Immunofluorescence staining showing H3R expression in both inner and outer HCs within the organ of Corti. b Negative control incubated only with the secondary antibody (Alexa Fluor™ 488) without the primary anti-H3R antibody. c High-magnification image illustrating H3R signals at the neurite terminals of SGNs near the HCs. d – e Representative images demonstrating H3R expression in SGNs and the corresponding negative control. f High-magnification image showing H3R localization in both the somata and neurites of SGNs. g – i No colocalization is observed between Ribeye and H3R, indicating the absence of H3R at ribbon synapses. H3R (green); neurofilament 200 (NF200, red in a–f); Ribeye (red in g–i); nuclei (DAPI, blue). Scale bars: 15 μm in a – c ; 20 μm in d , e , g ; 5 μm in f ; 10 μm in h , i

    Article Snippet: Nuclear staining was performed using ProLong Gold Antifade Mountant with DAPI (cat. #8961S, Cell Signaling Technology, USA).

    Techniques: Immunofluorescence, Staining, Expressing, Negative Control, Incubation

    Effects of H3R antagonist ciproxifan on cochlear hair cell (HC) morphology. a Schematic illustration of cochlear explant treatment with the H3R antagonists. b Representative image of the control group (0µM ciproxifan). c – e Cochlear explants were treated with ciproxifan at concentrations of 10µM, 50µM, and 100µM, respectively. Representative images shown are from the middle turn of the cochlea. HCs are labeled with phalloidin (red), and nuclei with DAPI (blue). Scale bars: 25 μm

    Journal: Neurochemical Research

    Article Title: Histamine H3 Receptor Antagonists Influence the Directional Growth of Type II Spiral Ganglion Neurites Within the Developing Cochlea of C57BL/6 Mice

    doi: 10.1007/s11064-025-04521-9

    Figure Lengend Snippet: Effects of H3R antagonist ciproxifan on cochlear hair cell (HC) morphology. a Schematic illustration of cochlear explant treatment with the H3R antagonists. b Representative image of the control group (0µM ciproxifan). c – e Cochlear explants were treated with ciproxifan at concentrations of 10µM, 50µM, and 100µM, respectively. Representative images shown are from the middle turn of the cochlea. HCs are labeled with phalloidin (red), and nuclei with DAPI (blue). Scale bars: 25 μm

    Article Snippet: Nuclear staining was performed using ProLong Gold Antifade Mountant with DAPI (cat. #8961S, Cell Signaling Technology, USA).

    Techniques: Control, Labeling

    Effects of H3R antagonist pitolisant on cochlear HCs. a Representative image of the control group (0µM pitolisant). b – d Cochlear explants treated with pitolisant at 10µM, 50µM, and 100µM, respectively. a 4 , b 4 , c 4 , d 4 High-magnification views of the boxed regions in A 3 -D 3 , respectively. e – f Quantification of IHCs and OHCs in the apical, middle, and basal turns showed no statistically significant differences between pitolisant-treated groups and controls ( n = 6 per group). Phalloidin (red), nuclei (DAPI, blue). Scale bars: 25 μm

    Journal: Neurochemical Research

    Article Title: Histamine H3 Receptor Antagonists Influence the Directional Growth of Type II Spiral Ganglion Neurites Within the Developing Cochlea of C57BL/6 Mice

    doi: 10.1007/s11064-025-04521-9

    Figure Lengend Snippet: Effects of H3R antagonist pitolisant on cochlear HCs. a Representative image of the control group (0µM pitolisant). b – d Cochlear explants treated with pitolisant at 10µM, 50µM, and 100µM, respectively. a 4 , b 4 , c 4 , d 4 High-magnification views of the boxed regions in A 3 -D 3 , respectively. e – f Quantification of IHCs and OHCs in the apical, middle, and basal turns showed no statistically significant differences between pitolisant-treated groups and controls ( n = 6 per group). Phalloidin (red), nuclei (DAPI, blue). Scale bars: 25 μm

    Article Snippet: Nuclear staining was performed using ProLong Gold Antifade Mountant with DAPI (cat. #8961S, Cell Signaling Technology, USA).

    Techniques: Control

    Dimethyl sulfoxide (DMSO) at experimental concentrations does not affect HC viability or morphology. a Representative image of the control group cultured in culture medium without DMSO, showing intact HC morphology. b – c Explants treated with 0.50% and 1.00% DMSO, respectively, exhibited no detectable HC loss or structural alterations. d – e Quantification of IHCs and OHCs in the apical, middle, and basal turns showed no statistically significant differences between DMSO-treated and control groups. Phalloidin (red), nuclei (DAPI, blue). ns > 0.05; n = 6 per group. Scale bar: 50 μm

    Journal: Neurochemical Research

    Article Title: Histamine H3 Receptor Antagonists Influence the Directional Growth of Type II Spiral Ganglion Neurites Within the Developing Cochlea of C57BL/6 Mice

    doi: 10.1007/s11064-025-04521-9

    Figure Lengend Snippet: Dimethyl sulfoxide (DMSO) at experimental concentrations does not affect HC viability or morphology. a Representative image of the control group cultured in culture medium without DMSO, showing intact HC morphology. b – c Explants treated with 0.50% and 1.00% DMSO, respectively, exhibited no detectable HC loss or structural alterations. d – e Quantification of IHCs and OHCs in the apical, middle, and basal turns showed no statistically significant differences between DMSO-treated and control groups. Phalloidin (red), nuclei (DAPI, blue). ns > 0.05; n = 6 per group. Scale bar: 50 μm

    Article Snippet: Nuclear staining was performed using ProLong Gold Antifade Mountant with DAPI (cat. #8961S, Cell Signaling Technology, USA).

    Techniques: Control, Cell Culture

    H3R antagonists induce misdirected neurite outgrowth in type II SGNs in cochlear explants. a Representative immunofluorescence images showing typical SGN innervation: type I SGNs project radially to IHCs, while type II SGNs extend longitudinally from the apex toward the base to innervate OHCs. b Cochlear explant treated with 50µM ciproxifan showing misdirected type II SGN neurites. c Cochlear explant treated with 50µM pitolisant showing a similar reversal of type II SGN projections. a 4 , b 4 , c 4 High-magnification views of the boxed regions in a 3 , b 3 , c 3 . White asterisks indicate misdirected neurites projecting toward the cochlear apex. d Percentage of misdirected type II SGNs following treatment with different concentrations of ciproxifan per 300 μm. Data are presented as mean ± SEM. Statistical analysis was performed using one-way ANOVA followed by Bonferroni’s test; ** p < 0.01. NF200 (green), phalloidin (red), DAPI (blue); n = 6 per group ( n = 24 in total). Scale bars: 50 μm in a 1–3 , b 1–3 , and c 1–3 ; 20 μm in a 4 , b 4 , and c 4

    Journal: Neurochemical Research

    Article Title: Histamine H3 Receptor Antagonists Influence the Directional Growth of Type II Spiral Ganglion Neurites Within the Developing Cochlea of C57BL/6 Mice

    doi: 10.1007/s11064-025-04521-9

    Figure Lengend Snippet: H3R antagonists induce misdirected neurite outgrowth in type II SGNs in cochlear explants. a Representative immunofluorescence images showing typical SGN innervation: type I SGNs project radially to IHCs, while type II SGNs extend longitudinally from the apex toward the base to innervate OHCs. b Cochlear explant treated with 50µM ciproxifan showing misdirected type II SGN neurites. c Cochlear explant treated with 50µM pitolisant showing a similar reversal of type II SGN projections. a 4 , b 4 , c 4 High-magnification views of the boxed regions in a 3 , b 3 , c 3 . White asterisks indicate misdirected neurites projecting toward the cochlear apex. d Percentage of misdirected type II SGNs following treatment with different concentrations of ciproxifan per 300 μm. Data are presented as mean ± SEM. Statistical analysis was performed using one-way ANOVA followed by Bonferroni’s test; ** p < 0.01. NF200 (green), phalloidin (red), DAPI (blue); n = 6 per group ( n = 24 in total). Scale bars: 50 μm in a 1–3 , b 1–3 , and c 1–3 ; 20 μm in a 4 , b 4 , and c 4

    Article Snippet: Nuclear staining was performed using ProLong Gold Antifade Mountant with DAPI (cat. #8961S, Cell Signaling Technology, USA).

    Techniques: Immunofluorescence