Journal: Cell reports

Article Title: Widespread sex-dimorphism across single-cell transcriptomes of adult African turquoise killifish tissues

doi: 10.1016/j.celrep.2023.113237

Figure Lengend Snippet: Key resource table

Article Snippet: 85 https://cran.r-project.org RUVSeq v1.20.0 Risso et al 86 https://github.com/drisso/RUVSeq scds v1.2.0 Bais et al 87 https://github.com/kostkalab/scds scProportionTest v0.0.0.9000 Miller et al 54 https://github.com/rpolicastro/scProportionTest scSorter v0.0.2 Guo et al 88 https://github.com/cran/scSorter SCTransform v0.3.2 Hafemeister et al 89 https://github.com/satijalab/sctransform scType 1.0 Ianevski et al 90 https://github.com/IanevskiAleksandr/sc-type scvelo v0.2.5 Bergen et al 91 https://github.com/theislab/scvelo Seurat v3.2.2 Satija et al, Butler et al, Stuart et al, Hao et al 92 – 95 https://github.com/satijalab/seurat/releases/tag/v3.2.2 SingleCellNet v0.1.0 Tan et al 96 https://github.com/pcahan1/singleCellNet velocyto v0.17.17 La Manno et al 44 https://github.com/velocyto-team/velocyto.py Other 10x Genomics User Guide Chromium Next GEM Single-cell 3′ Reagent Kits v3.1 10x Genomics Cat# CG000204 , Rev D 4200 TapeStation system Agilent Technologies Cat# G2991A 5424R Microcentrifuge Eppendorf Cat# 05-401-203 63x/1.4 Plan ApoChromat Oil DIC M27 Objective Zeiss Cat# 420782-9900-000 Beadbug 6 microtube homogenizer Benchmark Scientific Cat# D1036 Chromium Next GEM Chip G 10x Genomics Cat# 2000177 Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 10x Genomics Cat# PN-1000121 Countess Cell Counting Chamber Slides Thermo Fisher Scientific Cat# C10228 Countess II FL Automated Cell Counter Thermo Fisher Scientific Cat# AMQAX1000 Cryostat CM 1860 Leica Cat# 14-0491-46884 EasySep Dead Cell Removal (Annexin V) Kit STEMCELL Technologies Cat# 17899 Keyence BZ-X710 Keyence Unavailable Liver Dissociation Kit Miltenyi Biotec Cat# 130-105-807 Low Retention Pipette Tips USA Scientific Cat# 1183-1710 Lysing Matrix D tube MP Cat# 6913500 MACSQuant Analyzer 10 Miltenyi Biotec Cat#130-096-343 Magnetic Induction Cycler (MIC) machine Bio Molecular Systems Cat# MIC-2 PTFE-coated microtome blades Duraedge Cat# 7223 Qubit ® 3.0 Fluorometer Thermo Fisher Scientific Cat# Q33216 RNAscope ™ Multiplex Fluorescent Reagent Kit v2 With Sample Preparation and Pretreatment User Guide Advanced Cell Diagnostics UM323100 SensiFAST SYBR ® No-ROX Kit Bioline Cat# BIO-98020 Stellaris 5 Confocal Microscope Leica NA Superfrost Plus Micro Slides VWR Cat# 48311-703 Thermal cycler C1000 Bio-Rad Cat# 1851196 Open in a separate window Key resource table

Techniques: Recombinant, Modification, RNAscope, Staining, Quantitation Assay, Sensitive Assay, Multiplex Assay, Control, Microscopy, Software, Cell Counting, Transferring, Sample Prep