Journal: eLife

Article Title: Cardiac endothelial cells maintain open chromatin and expression of cardiomyocyte myofibrillar genes

doi: 10.7554/elife.55730

Figure Lengend Snippet: Figure 2. Expression of at least one CMF gene is seen in ~59% of cardiac ECs. (A): Analysis of mouse heart and lung single cell data from Tabula Muris in Schaum, et al (Nature, 2018). Fifteen cardiac myofibrillar (CMF) genes were chosen based on high, unique expression in the cardiomyocyte cell subsets. Positive expression was determined as a normalized count (ln(1+Counts-per-million)) greater than or equal to one. (B): Percentage of cardiomyocytes vs endothelial cells or fibroblasts within the heart and lung that express 1–15 of the selected CMF genes. (C–E). Analysis of unspliced vs spliced transcripts in Tabula Muris data. Data shown are merged counts for all cells within the cardiomyocyte (CM), endothelial cell (EC), or fibroblast Figure 2 continued on next page

Article Snippet: DOI: https://doi.org/10.7554/eLife.55730 12 of 19 Continued Reagent type (species) or resource Designation Source or reference Identifiers Additional information Software, algorithm Genrich https://github.com/jsh58/Genrich Software, algorithm Picard Tools http://broadinstitute.github.io/picard/ Software, algorithm samtools Li et al., 2009 Software, algorithm STAR Dobin, 2013 Software, algorithm Seurat Stuart et al., 2019 Software, algorithm R https://www.r-project.org/ Software, algorithm DiffBind Ross-Innes et al., 2012 Software, algorithm Deeptools Ramı́rez et al., 2016 Software, algorithm Homer Heinz et al., 2010 Software, algorithm Velocyto La Manno et al., 2018 Other DAPI stain Molecular Probes (1:1000) Other RNAscope Probe- MmTnnt2-C3 ACD Bio Cat# 418681-C3 Other RNAscope Probe- MmCdh5-C2 ACDBio Cat# 312531-C2 Commercial assay or kit RNAscope Multiplex Fluorescent v2 Assay ACD Bio Cat# 323136 Commercial assay or kit Illumina Tagment DNA Enzyme and Buffer Illumina Cat#:20034197 1.25 uL of enzyme used per 50,000 nuclei for transposition

Techniques: Expressing

Journal: Cell stem cell

Article Title: Organoids model transcriptional hallmarks of oncogenic KRAS activation in lung epithelial progenitor cells

doi: 10.1016/j.stem.2020.07.022

Figure Lengend Snippet: KEY RESOURCES TABLE

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

Techniques: Virus, Plasmid Preparation, Recombinant, Multiplex Assay, Lysis, Reverse Transcription, Mass Spectrometry, Gene Expression, Software, Saline, Gentle, Modification