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: (A) Schematic for tissue dissociation and sequencing. Blood, kidneys, livers, and spleens were isolated from 3 cohorts of 3–4 fish. Solid tissues were dissociated into single-cell suspensions. Single-cell RNA-seq libraries were made using the 10x Genomics protocol. (B-F) UMAP plots of the killifish tissue atlas denoted by (B) annotated cell type, (C) tissue of origin, (D) sex, (E) cohort, and (F) RNA velocity. (G) Expression UMAP for canonical marker genes for B-cells, macrophages, neutrophils, and hepatocytes. (H) Dotplot of marker gene expression, showing average expression level and percentage of cells expressing each marker gene. Markers of cell proliferation (pcna and mki67) are provided under a yellow overlay, since they were used to annotated proliferative states. Since many NCBI gene names were uninformative, names corresponding to predicted homologs are used. Original NCBI gene names are provided in Supplementary Table S11. HSPCs: hematopoietic stem and progenitor cells. See also Supplementary Figure S1.

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 TM 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: Sequencing, Isolation, RNA Sequencing, Expressing, Marker, Gene Expression

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 TM 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, cDNA Synthesis, Control, Microscopy, Software, Cell Counting, Transferring, Sample Prep