Journal: Cell systems

Article Title: Rare cell detection by single cell RNA sequencing as guided by single molecule RNA FISH

doi: 10.1016/j.cels.2018.01.014

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies mouse anti-EGFR antibody, clone 225 Millipore MABF120 anti-mouse IgG-Alexa Fluor488 Jackson Laboratories 715-545-150 anti-NGFR APC-labelled clone ME20.4 Biolegend 345107 Bacterial and Virus Strains N/A N/A N/A Biological Samples N/A N/A N/A Chemicals, Peptides, and Recombinant Proteins N/A N/A N/A Critical Commercial Assays C1 single cell mRNA seq IFC Fluidigm 100–5760 NEBNext Poly(A) mRNA Magnetic Isolation Module NEB E7490S NEBNext Ultra RNA Library Prep Kit for Illumina NEB E7530S Deposited Data Raw Single cell RNA seq data this paper https://www.dropbox.com/sh/tjdv3mgxle30qiv/AAAXdnYJRZzMeZYaQg7YIUUaa?dl=0 ; GSE99330 Raw Bulk RNA seq data Shaffer et al. 2017 https://www.dropbox.com/s/ir7fp9ragta8jan/A6_bulk_NoDrugfastq.gz?dl=0 RNA FISH data Shaffer et al. 2017 https://www.dropbox.com/s/om8uq3z3lxnfdtk/fishSubset.txt?dl=0 Experimental Models: Cell Lines WM989 Meenhard Herlyn N/A NIH 3T3 Raj Lab N/A JC4 Raj Lab N/A Experimental Models: Organisms/Strains N/A N/A N/A Oligonucleotides RNA FISH Probe sequences Biosearch Technologies Supplementary Table 4 Recombinant DNA N/A N/A N/A Software and Algorithms RNA FISH image analysis software Raj Lab https://bitbucket.org/arjunrajlaboratory/rajlabimagetools/wiki/Dentist scRNA-seq analysis code This paper https://www.dropbox.com/sh/scmiu1tbrsxupto/AACTL5iWaW-zxRmAbFXnIwnMa?dl=0 Drop-seq_tools-1.0.1 McCaroll Lab http://mccarrolllab.com/dropseq/ STAR version 2.4.2a https://github.com/alexdobin/STAR/releases mRNASeqHT_demultiplex.pl https://www.fluidigm.com/c1openapp/scripthub/script/2015-08/mrna-seq-ht-1440105180550-2 HTSeq https://pypi.python.org/pypi/HTSeq Other N/A N/A N/A Open in a separate window KEY RESOURCES TABLE - Estimates of rare cell gene expression vary with transcriptome coverage - The no. of cells analyzed also affects estimates of rare cell gene expression - In rare cell analysis, cell coverage has a larger effect than the no. of cells used - Internal and external controls guide selection of transcriptome coverage thresholds

Techniques: Recombinant, Isolation, RNA Sequencing Assay, Software

Journal: Cell stem cell

Article Title: A drug screen using human iPSC-derived hepatocyte-like cells identifies cardiac glycosides as a potential treatment for hypercholesterolemia

doi: 10.1016/j.stem.2017.01.011

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Spectrum Collection; CAS 104227-87-4 Ouabain Octahydrate MicroSource Discovery Systems, Inc. 01500676; CAS 11018-89-6, 630-60-4 Cycloheximide Sigma-Aldrich C1988; CAS ‘66-81-9 MG132 Selleck Chemicals S2619; CAS 133407-82-6 Dimethyl sulfoxide Sigma-Aldrich D8418; CAS 67-68-5 CuRx TM Nitisinone Yecuris Corporation 20-0027; CAS 104206-65-7 Critical Commercial Assays RNeasy mini Kit Qiagen 74106 TURBO DNA-free TM Kit ThermoFisher/Ambion AM1907 M-MLV Reverse Transcriptase ThermoFisher/Invitrogen 28025-013 TaqMan ® Gene Expression ThermoFisher/Applied Biosystems 4369016 Power SYBR Green ThermoFisher/Applied Biosystems 4367659 Human apoB ELISA development kit (HRP) MabTech, Inc 3715-1H-20 Deposited Data – N/A Experimental Models: Cell Lines HoFH iPSC-JD4 Stephen Duncan { Cayo et al., 2012 , Hepatology, 56, 2163-71} Wild type iPSC-K3 Stephen Duncan { Si-Tayeb et al., 2010 , BMC Dev Biol, 10, 81} Wild type iPSC-SV20 Wenli Yang {Yang et al., 2015, PLoS One, 10, e0134995} Female Primary Hepatocytes ThermoFisher/Life Technologies #Hu1475 Male Primary Hepatocytes Celsis In Vitro Technologies/Bioreclamation, LLC #M00995 HepG2 cells ATCC #HB-8065 Experimental Models: Organisms/Strains Mouse: FRGN; Fah−/−/Rag2−/−/Il2rg−/− NOD Markus Grompe { Wilson et al., 2014 , Stem Cell Res, 13, 404-12} Recombinant DNA – N/A Sequence-Based Reagents Primetime Assay apoB 56-FAM/CT GGA TAC C/Zen/G TGT ATG GAA ACT GCT CC/3IABkFQ/ Primer 1-CAT TGC CCT TCC TCG TCT T Primer 2-CCA GAG ACA GAA GAA GCC AAG Integrated DNA Technologies Hs.PT.47.18897448 Primetime Assay rpl13 56-FAM/AGCAGTACC/ZEN/TGTTTAGCCACGATGG/3IABkFQ Primer 1-GCCTTCACAGCGTACGA Primer 2-CGAAGATGGCGGAGGTG Integrated DNA Technologies Hs.PT.58.1788586 Software and Algorithms Microsoft Excel for Mac v15.29 Microsoft Adobe Illustrator CS6 Adobe Systems Inc Adobe Photoshop CS6 Adobe Systems Inc Image Lab software Bio-Rad 1709691 Graphpad Prism v6 Graphpad Software, Inc Other Spectrum Collection Microsource Discovery Systems Inc http://www.msdiscovery.com/spectrum.html Hepatocyte Thaw Medium ThermoFisher Scientific CM7500 Williams’ Medium E Sigma-Aldrich W4128 HCM BulletKit (CC-3199 & CC-4182) Lonza CC-3198 Open in a separate window KEY RESOURCES TABLE

Techniques: Recombinant, Purification, Reverse Transcription, Gene Expression, SYBR Green Assay, Enzyme-linked Immunosorbent Assay, In Vitro, Sequencing, Software