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. 2023 Jun 20;3(7):100346. doi: 10.1016/j.xgen.2023.100346
REAGENT or RESOURCE SOURCE IDENTIFIER
Biological samples
Human adipose-derived mesenchymal stem cells Munich Obesity BioBank (MOBB) NA
Primary human hepatocytes BioIVT YNZ
Chemicals, peptides, and recombinant proteins
MitoTracker™ Deep Red FM Molecular Probes, Inc. M22426
BODIPY™ 505/515 Molecular Probes, Inc. D3921
Alexa Fluor™ 568 Phalloidin Life Technologies Corp. A12380
Hoechst 33342 Molecular Probes, Inc. H3570
Wheat Germ Agglutinin, Alexa Fluor™ 555 Conjugate Molecular Probes, Inc. W32464
SYTO™ 14 Green Fluorescent Nucleic Acid Stain Molecular Probes, Inc. S7576
16% Paraformaldehyde, methanol-free Electron Microscopy Sciences 15710-S
Hank’s Balanced Salt Solution (1x), HBSS Life Technologies Corp. 14025076
Triton X-100 Merck KGaA X100
Phalloidin-Atto-565 Merck KGaA 94072
Critical commercial assays
Infinium HTS assay + GSA Bead Chips Illumina, Inc. NA
Deposited data
Raw data and code GitHub https://github.com/ClaussnitzerLab/Lipocyte-Profiler
Experimental models: Cell lines
hWAT Xue et al.29 https://doi.org/10.1038/nm.3881
hBAT Xue et al.29 https://doi.org/10.1038/nm.3881
SGBS Wabitsch et al. 2001 https://doi.org/10.1038/sj.ijo.0801520
Cas9 expressing hWAT This paper NA
Oligonucleotides
guide sequences targeting:
PPARG: ATACACAGGTGCAATCAAAG and CAACTTTGGGATCAGCTCCG;
PPARGC1A TATTGAACGCACCTTAAGTG and AGTCCTCACTGGTGGACACG;
MFN1: CACCAGGTCATCTCTCAAGA and TTATATGGCCAATCCCACTA;
PLIN1: TCACGGCAGATACTTACCAG and TCTGCACGGTGTATCGAGAG;
INSR: TTATCGGCGATATGGTGATG and AGTGAGTATGAGGATTCGGC;
IRS1 CCCAGGACCCGCATTCAAAG and CCGAAGCACTAGATCGCCGT		 This paper NA
non-targeted controls (control guide sequences):
ATCAGGCCTTGTCCGTGATT; TACGTCATTAAGAGTTCAAC; GACAGTGAAATTAGCTCCCA; GATTCATACTAAACACTCTAx; CCTAGTTCATAAGCTACGCC		 This paper NA
Software and algorithms
LipocyteProfiler This paper https://github.com/ClaussnitzerLab/Lipocyte-Profiler
CRISPResso Pinello et al.68 https://doi.org/10.1038/nbt.3583
PLINK Purcell et al.69 and Chang et al. 2015 https://doi.org/10.1086/519795 and https://doi.org/10.1186/s13742-015-0047-8
SHAPEIT2 Delaneau et al.70 https://doi.org/10.1038/nmeth.2307
PRS-CS Ge et al.71 https://doi.org/10.1038/s41467-019-09718-5
LDpred Vilhjálmsson et al.72 https://doi.org/10.1016/j.ajhg.2015.09.001
igraph Csardi et al. 2006 https://igraph.org
Enrichr Chen et al. 2013 https://maayanlab.cloud/Enrichr/
FastQC Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
STAR Dobin et al.73 https://doi.org/10.1093/bioinformatics/bts635
DESeq2 Love et al.74 https://doi.org/10.1186/s13059-014-0550-8
CellProfiler 3.1.9 Carpenter et al. 2006 https://doi.org/10.1186/gb-2006-7-10-r100
Harmony 4.9 PerkinElmer Inc. HH17000010
ARACNE Margolin et al.75 https://doi.org/10.1186/1471-2105-7-S1-S7
UMAP R package 0.2.7.0 McInnes et al.76 https://doi.org/10.21105/joss.00861
ComplexHeatmap Bioconductor package 2.7.7 Gu et al.77 https://doi.org/10.1093/bioinformatics/btw313
Sample Progression Discovery (SPD) Qui et al. 2011 https://doi.org/10.1371/journal.pcbi.1001123.g001
BEclear Akulenko et al.78 https://doi.org/10.1371/journal.pone.0159921
R 3.6.1 The R Foundation for Statistical Computing NA
Other
CellCarrier Ultra 96 well plate, black (now: PhenoPlate™ 96-well) PerkinElmer Inc. #6005550
CellCarrier Ultra 96 well plate, black (now: PhenoPlate™ 96-well); collagen-coated PerkinElmer Inc. #6055700
Opera Phenix® High-Content Screening System PerkinElmer Inc. NA
Leica DMi8 microscope with HC PL APO ×63/1.40 oil objective Leica Microsystems GmbH NA
MGB Biobank data Partners HealthCare hospitals NA