other:
Recombinant:Article Title: On the origin of metastases: Induction of pro-metastatic states after impending cell death via ER stress, reprogramming, and a cytokine storm.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies BrdU antibody University of Iowa Hybridoma Bank Cat# G3G4 Cleaved Caspase 3 (D175) antibody Cell Signaling Cat# 9661L Chemicals, peptides, and recombinant proteins DMEM/F12 Sigma Aldrich Cat# D8062 MEM Sigma Aldrich Cat# M4655 RPMI Sigma Aldrich Cat# R0883 Puromycin GIBCO Cat# A11138-03 TRIzol Ambion Cat# 15596018 PFA AppliChem Cat# A3813 X-Gal AppliChem Cat# A1007,0001 BCIP/NBT Sigma Aldrich Cat# B5655 DMSO Sigma Aldrich Cat# G1640 Staurosporine Apexbio Cat# A8192 Q-VD-OPh Apexbio Cat# A1901 DIDS Apexbio Cat# B7675 5FU Sigma Aldrich Cat# F6627 Oxaliplatin Sigma Aldrich Cat# O9512 Selumetinib gift from P. Nowak N/A Vemurafenib Selleckchem Cat# S1267 DAPI Sigma Aldrich Cat# D9542 Reparixin Selleckchem Cat# S8640 ISO-1 Selleckchem Cat# S7732 Cetuximab BiovVsion Cat# A1047-100 Regorafenib Selleckchem Cat# S1178 AZD-5069 Selleckchem Cat# S6645 Valdecoxib Selleckchem Cat# S4049 Human recombinant CXCL8 R&D Systems Cat# 208-IL Human recombinant CXCL1 R&D Systems Cat# 275-GR Human recombinant IL-32a R&D Systems Cat# 3040-IL Human recombinant IL-32g R&D Systems Cat# 4690-IL Human recombinant Amphiregulin STEMCELL Technologies Cat# 78104 Bafilomycin A1 InvivoGen Cat# tlrl-baf1 C12FDG Setareh Biotech Cat# 7188 Tunicamycin Sigma Aldrich Cat# T7765 MKC-3946 Selleckchem Cat# S8286 GSK2606414 Selleckchem Cat# S7307 EdU Lumiprobe Cat# 10540 Sulfo-Cy3-Azide Lumiprobe Cat# A1330 Critical commercial assays iQ SYBR super mix BioRad Cat# 1708882 Superscript II Invitrogen Cat# 18064-014 Truecut CAS9 protein V2 Thermofisher Cat# A36498 Geneart genome clivage detection kit Thermofisher Cat# A24372 Trueguide TracrRNA Thermofisher Cat# A35506 (Continued on next page) e1 Cell Reports 38, 110490, March 8, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Trueguide crRNA Thermofisher Cat# A35512 Pierce protein concentrator Thermo Scientific Cat# 88522 Human L507 Array, Membrane RayBiotech Cat# AAH-BLM-1A-2 Proteome Profiler Human XLCytokine Array Kit R&D Systems Cat# ARY022B InFusion HD Cloning kit Takara Bio Cat# 102518 CloneAmp HiFi premix kit Takara Bio Cat# 639298 Deposited data Transcriptome analysis of PAMEs This paper GEO: GSE171543 Transcriptome analysis of PIMs This paper GEO: GSE171560 Spiked-single cell RNAseq analysis of CC14 Bernal et al., 2020 PRJNA611719 Experimental models: Cell lines CC14 and derived clones Primary culture made in the lab (Varnat et al., 2009; Bernal et al., 2020) N/A CC36 Primary culture made in the lab (Varnat et al., 2009) N/A
Article Title: Developmental Analysis of Bone Marrow Neutrophils Reveals Populations Specialized in Expansion, Trafficking, and Effector Functions.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-human CD11b (Clone ICRF44) Biolegend Cat#301312; RRID: AB_314164 Anti-human CD16 (Clone 3G8) Fluidigm Cat#329002B Bacterial and Virus Strains DH5a Escherichia coli GFP (Chua and Wong, 2013) N/A Chemicals, Peptides, and Recombinant Proteins 1X RBC Lysis Buffer eBioscience Cat# 00-4333-57 5-Iodo-20-deoxyuridine (IdU) Sigma-Aldrich Cat# I7125 5–Fluorouracil Sigma-Aldrich Cat# F6627 Cisplatin Sigma-Aldrich Cat# 479306-1G CountBright Absolute Counting Beads Life Technologies Cat# C36950 DAPI Life Technologies Cat# D1306 Hema 3 Manual Staining System Thermo Fisher Cat# 22-122911 Dihydrorhodamine 123 Molecular Probes Cat# D23806 EQ Four Element Calibration Beads Fluidigm Cat# 201078 Human G-CSF (Neupogen) Amgen Cat# 100696800 Iridium Interchelator Fluidigm Cat# 201192B Dimethyl sulphoxide Sigma-Aldrich Cat# D5879 Paraformaldehyde Sigma-Aldrich Cat# 158127 Fixation/Permeabilization solution kit BD Bioscience Cat# 554714 Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat# P1585 Matrigel matrix growth factor reduced BD Bioscience Cat# 354230 Bovine Serum Albumin, lyophilized powder Sigma-Aldrich Cat# A2058 Evans Blue Sigma-Aldrich Cat# 46160 Trypticase Soy Agar (TSA II) with 5% Sheep Blood Thermo Fisher Cat# 221261 MethoCult M3134 Stem Cell Technologies Cat#03134 Iscove’s Modified Dulbecco’s Medium (IMDM) with 25mM HEPES Stem Cell Technologies Cat#361150 Anti-BSA Sigma-Aldrich Cat# B7276 Critical Commercial Assays RapiClear 1.55 Sunjin Lab Cat# RC155001 Zombie UV fixable viability kit Biolegend Cat# 423108 Arcturus PicoPure RNA isolation kit Thermo Fisher Cat# KIT0214 ERCC RNA Spike-In Mix Thermo Fisher Cat# 4456740 BrdU kit BD Biosciences Cat# 559619; RRID: AB_2617060 Deposited Data Raw RNA-seq data This Paper GEO: GSE109467 Experimental Models: Organisms/Strains Mouse: C57BL/6J The Jackson Laboratory Stock No: 000664 Mouse: Lyz2cre/cre: B6.129P2-Lyz2tm1(cre)Ifo/J The Jackson Laboratory Stock No: 004781 Mouse: S100a8cre: B6.Cg-Tg(S100A8-cre,-EGFP)1Ilw/J The Jackson Laboratory Stock No: 021614 Mouse: Rosa26mT/mG: STOCK Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J The Jackson Laboratory Stock No: 007676 Mouse: Cxcl12DsRed/+: STOCK Cxcl12tm2.1Sjm/J The Jackson Laboratory Stock No: 022458 Mouse: Rosa26LsL-YFP: B6.129X1-Gt(ROSA)26Sortm1(EYFP)Cos/J The Jackson Laboratory Stock No: 006148 Mouse: Albino B6: B6(Cg)-Tyrc-2J/J The Jackson Laboratory Stock No: 000104 Mouse: Cxcr4fl/fl: B6.129P2-Cxcr4tm2Yzo/J The Jackson Laboratory Stock No: 008767 (Continued on next page) e3 Immunity 48, 364–379.e1–e8, February 20, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse: Fucci-S/G2/M (#474) RIKEN BRC, Ibaraki, Japan Stock No: RBRC02704 Mouse: Fucci-G1 (#639) RIKEN BRC, Ibaraki, Japan Stock No: RBRC02709 Mouse: Lyz2gfp/+ (Lyz2tm1.1Graf) Thomas Graf, (Faust et al., 2000) N/A Mouse: Cxcr4WHIM (Cxcr41013/+) Françoise Bachelerie, (Balabanian et al., 2012) N/A Mouse: Cebpe / Philip H. Koeffler (Kyme et al., 2012) N/A Software and Algorithms Imaris Bitplane http://www.bitplane.com/imaris/imaris GraphPad Prism 7 GraphPad Software http://www.graphpad.com Cytofkit 1.6.5 Bioconductor https://bioconductor.org/packages/release/ bioc/html/cytofkit.html FlowJo 10 TreeStar http://flowjo.com/ FIJI (Fiji is just ImageJ) NIH http://imagej.nih.gov/ij Photoshop CS6 Adobe https://www.adobe.com/ t-SNE (van der Maaten and Hinton, 2008) https://cran.r-project.org/web/packages/ Rtsne/index.html MATLAB Mathworks https://www.mathworks.com/products/ matlab.html edgeR Bioconductor https://bioconductor.org/packages/ release/bioc/html/edgeR.html pheatmap R package https://cran.r-project.org/web/ packages/pheatmap/index.html Seriation (Hahsler et al., 2008) https://cran.r-project.org/web/packages/ seriation/index.html Enrichr (Chen et al., 2013) http://amp.pharm.mssm.edu/Enrichr/
Virus:Article Title: Developmental Analysis of Bone Marrow Neutrophils Reveals Populations Specialized in Expansion, Trafficking, and Effector Functions.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-human CD11b (Clone ICRF44) Biolegend Cat#301312; RRID: AB_314164 Anti-human CD16 (Clone 3G8) Fluidigm Cat#329002B Bacterial and Virus Strains DH5a Escherichia coli GFP (Chua and Wong, 2013) N/A Chemicals, Peptides, and Recombinant Proteins 1X RBC Lysis Buffer eBioscience Cat# 00-4333-57 5-Iodo-20-deoxyuridine (IdU) Sigma-Aldrich Cat# I7125 5–Fluorouracil Sigma-Aldrich Cat# F6627 Cisplatin Sigma-Aldrich Cat# 479306-1G CountBright Absolute Counting Beads Life Technologies Cat# C36950 DAPI Life Technologies Cat# D1306 Hema 3 Manual Staining System Thermo Fisher Cat# 22-122911 Dihydrorhodamine 123 Molecular Probes Cat# D23806 EQ Four Element Calibration Beads Fluidigm Cat# 201078 Human G-CSF (Neupogen) Amgen Cat# 100696800 Iridium Interchelator Fluidigm Cat# 201192B Dimethyl sulphoxide Sigma-Aldrich Cat# D5879 Paraformaldehyde Sigma-Aldrich Cat# 158127 Fixation/Permeabilization solution kit BD Bioscience Cat# 554714 Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat# P1585 Matrigel matrix growth factor reduced BD Bioscience Cat# 354230 Bovine Serum Albumin, lyophilized powder Sigma-Aldrich Cat# A2058 Evans Blue Sigma-Aldrich Cat# 46160 Trypticase Soy Agar (TSA II) with 5% Sheep Blood Thermo Fisher Cat# 221261 MethoCult M3134 Stem Cell Technologies Cat#03134 Iscove’s Modified Dulbecco’s Medium (IMDM) with 25mM HEPES Stem Cell Technologies Cat#361150 Anti-BSA Sigma-Aldrich Cat# B7276 Critical Commercial Assays RapiClear 1.55 Sunjin Lab Cat# RC155001 Zombie UV fixable viability kit Biolegend Cat# 423108 Arcturus PicoPure RNA isolation kit Thermo Fisher Cat# KIT0214 ERCC RNA Spike-In Mix Thermo Fisher Cat# 4456740 BrdU kit BD Biosciences Cat# 559619; RRID: AB_2617060 Deposited Data Raw RNA-seq data This Paper GEO: GSE109467 Experimental Models: Organisms/Strains Mouse: C57BL/6J The Jackson Laboratory Stock No: 000664 Mouse: Lyz2cre/cre: B6.129P2-Lyz2tm1(cre)Ifo/J The Jackson Laboratory Stock No: 004781 Mouse: S100a8cre: B6.Cg-Tg(S100A8-cre,-EGFP)1Ilw/J The Jackson Laboratory Stock No: 021614 Mouse: Rosa26mT/mG: STOCK Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J The Jackson Laboratory Stock No: 007676 Mouse: Cxcl12DsRed/+: STOCK Cxcl12tm2.1Sjm/J The Jackson Laboratory Stock No: 022458 Mouse: Rosa26LsL-YFP: B6.129X1-Gt(ROSA)26Sortm1(EYFP)Cos/J The Jackson Laboratory Stock No: 006148 Mouse: Albino B6: B6(Cg)-Tyrc-2J/J The Jackson Laboratory Stock No: 000104 Mouse: Cxcr4fl/fl: B6.129P2-Cxcr4tm2Yzo/J The Jackson Laboratory Stock No: 008767 (Continued on next page) e3 Immunity 48, 364–379.e1–e8, February 20, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse: Fucci-S/G2/M (#474) RIKEN BRC, Ibaraki, Japan Stock No: RBRC02704 Mouse: Fucci-G1 (#639) RIKEN BRC, Ibaraki, Japan Stock No: RBRC02709 Mouse: Lyz2gfp/+ (Lyz2tm1.1Graf) Thomas Graf, (Faust et al., 2000) N/A Mouse: Cxcr4WHIM (Cxcr41013/+) Françoise Bachelerie, (Balabanian et al., 2012) N/A Mouse: Cebpe / Philip H. Koeffler (Kyme et al., 2012) N/A Software and Algorithms Imaris Bitplane http://www.bitplane.com/imaris/imaris GraphPad Prism 7 GraphPad Software http://www.graphpad.com Cytofkit 1.6.5 Bioconductor https://bioconductor.org/packages/release/ bioc/html/cytofkit.html FlowJo 10 TreeStar http://flowjo.com/ FIJI (Fiji is just ImageJ) NIH http://imagej.nih.gov/ij Photoshop CS6 Adobe https://www.adobe.com/ t-SNE (van der Maaten and Hinton, 2008) https://cran.r-project.org/web/packages/ Rtsne/index.html MATLAB Mathworks https://www.mathworks.com/products/ matlab.html edgeR Bioconductor https://bioconductor.org/packages/ release/bioc/html/edgeR.html pheatmap R package https://cran.r-project.org/web/ packages/pheatmap/index.html Seriation (Hahsler et al., 2008) https://cran.r-project.org/web/packages/ seriation/index.html Enrichr (Chen et al., 2013) http://amp.pharm.mssm.edu/Enrichr/
Red Blood Cell Lysis:Article Title: Developmental Analysis of Bone Marrow Neutrophils Reveals Populations Specialized in Expansion, Trafficking, and Effector Functions.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-human CD11b (Clone ICRF44) Biolegend Cat#301312; RRID: AB_314164 Anti-human CD16 (Clone 3G8) Fluidigm Cat#329002B Bacterial and Virus Strains DH5a Escherichia coli GFP (Chua and Wong, 2013) N/A Chemicals, Peptides, and Recombinant Proteins 1X RBC Lysis Buffer eBioscience Cat# 00-4333-57 5-Iodo-20-deoxyuridine (IdU) Sigma-Aldrich Cat# I7125 5–Fluorouracil Sigma-Aldrich Cat# F6627 Cisplatin Sigma-Aldrich Cat# 479306-1G CountBright Absolute Counting Beads Life Technologies Cat# C36950 DAPI Life Technologies Cat# D1306 Hema 3 Manual Staining System Thermo Fisher Cat# 22-122911 Dihydrorhodamine 123 Molecular Probes Cat# D23806 EQ Four Element Calibration Beads Fluidigm Cat# 201078 Human G-CSF (Neupogen) Amgen Cat# 100696800 Iridium Interchelator Fluidigm Cat# 201192B Dimethyl sulphoxide Sigma-Aldrich Cat# D5879 Paraformaldehyde Sigma-Aldrich Cat# 158127 Fixation/Permeabilization solution kit BD Bioscience Cat# 554714 Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat# P1585 Matrigel matrix growth factor reduced BD Bioscience Cat# 354230 Bovine Serum Albumin, lyophilized powder Sigma-Aldrich Cat# A2058 Evans Blue Sigma-Aldrich Cat# 46160 Trypticase Soy Agar (TSA II) with 5% Sheep Blood Thermo Fisher Cat# 221261 MethoCult M3134 Stem Cell Technologies Cat#03134 Iscove’s Modified Dulbecco’s Medium (IMDM) with 25mM HEPES Stem Cell Technologies Cat#361150 Anti-BSA Sigma-Aldrich Cat# B7276 Critical Commercial Assays RapiClear 1.55 Sunjin Lab Cat# RC155001 Zombie UV fixable viability kit Biolegend Cat# 423108 Arcturus PicoPure RNA isolation kit Thermo Fisher Cat# KIT0214 ERCC RNA Spike-In Mix Thermo Fisher Cat# 4456740 BrdU kit BD Biosciences Cat# 559619; RRID: AB_2617060 Deposited Data Raw RNA-seq data This Paper GEO: GSE109467 Experimental Models: Organisms/Strains Mouse: C57BL/6J The Jackson Laboratory Stock No: 000664 Mouse: Lyz2cre/cre: B6.129P2-Lyz2tm1(cre)Ifo/J The Jackson Laboratory Stock No: 004781 Mouse: S100a8cre: B6.Cg-Tg(S100A8-cre,-EGFP)1Ilw/J The Jackson Laboratory Stock No: 021614 Mouse: Rosa26mT/mG: STOCK Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J The Jackson Laboratory Stock No: 007676 Mouse: Cxcl12DsRed/+: STOCK Cxcl12tm2.1Sjm/J The Jackson Laboratory Stock No: 022458 Mouse: Rosa26LsL-YFP: B6.129X1-Gt(ROSA)26Sortm1(EYFP)Cos/J The Jackson Laboratory Stock No: 006148 Mouse: Albino B6: B6(Cg)-Tyrc-2J/J The Jackson Laboratory Stock No: 000104 Mouse: Cxcr4fl/fl: B6.129P2-Cxcr4tm2Yzo/J The Jackson Laboratory Stock No: 008767 (Continued on next page) e3 Immunity 48, 364–379.e1–e8, February 20, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse: Fucci-S/G2/M (#474) RIKEN BRC, Ibaraki, Japan Stock No: RBRC02704 Mouse: Fucci-G1 (#639) RIKEN BRC, Ibaraki, Japan Stock No: RBRC02709 Mouse: Lyz2gfp/+ (Lyz2tm1.1Graf) Thomas Graf, (Faust et al., 2000) N/A Mouse: Cxcr4WHIM (Cxcr41013/+) Françoise Bachelerie, (Balabanian et al., 2012) N/A Mouse: Cebpe / Philip H. Koeffler (Kyme et al., 2012) N/A Software and Algorithms Imaris Bitplane http://www.bitplane.com/imaris/imaris GraphPad Prism 7 GraphPad Software http://www.graphpad.com Cytofkit 1.6.5 Bioconductor https://bioconductor.org/packages/release/ bioc/html/cytofkit.html FlowJo 10 TreeStar http://flowjo.com/ FIJI (Fiji is just ImageJ) NIH http://imagej.nih.gov/ij Photoshop CS6 Adobe https://www.adobe.com/ t-SNE (van der Maaten and Hinton, 2008) https://cran.r-project.org/web/packages/ Rtsne/index.html MATLAB Mathworks https://www.mathworks.com/products/ matlab.html edgeR Bioconductor https://bioconductor.org/packages/ release/bioc/html/edgeR.html pheatmap R package https://cran.r-project.org/web/ packages/pheatmap/index.html Seriation (Hahsler et al., 2008) https://cran.r-project.org/web/packages/ seriation/index.html Enrichr (Chen et al., 2013) http://amp.pharm.mssm.edu/Enrichr/
Staining:Article Title: Developmental Analysis of Bone Marrow Neutrophils Reveals Populations Specialized in Expansion, Trafficking, and Effector Functions.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-human CD11b (Clone ICRF44) Biolegend Cat#301312; RRID: AB_314164 Anti-human CD16 (Clone 3G8) Fluidigm Cat#329002B Bacterial and Virus Strains DH5a Escherichia coli GFP (Chua and Wong, 2013) N/A Chemicals, Peptides, and Recombinant Proteins 1X RBC Lysis Buffer eBioscience Cat# 00-4333-57 5-Iodo-20-deoxyuridine (IdU) Sigma-Aldrich Cat# I7125 5–Fluorouracil Sigma-Aldrich Cat# F6627 Cisplatin Sigma-Aldrich Cat# 479306-1G CountBright Absolute Counting Beads Life Technologies Cat# C36950 DAPI Life Technologies Cat# D1306 Hema 3 Manual Staining System Thermo Fisher Cat# 22-122911 Dihydrorhodamine 123 Molecular Probes Cat# D23806 EQ Four Element Calibration Beads Fluidigm Cat# 201078 Human G-CSF (Neupogen) Amgen Cat# 100696800 Iridium Interchelator Fluidigm Cat# 201192B Dimethyl sulphoxide Sigma-Aldrich Cat# D5879 Paraformaldehyde Sigma-Aldrich Cat# 158127 Fixation/Permeabilization solution kit BD Bioscience Cat# 554714 Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat# P1585 Matrigel matrix growth factor reduced BD Bioscience Cat# 354230 Bovine Serum Albumin, lyophilized powder Sigma-Aldrich Cat# A2058 Evans Blue Sigma-Aldrich Cat# 46160 Trypticase Soy Agar (TSA II) with 5% Sheep Blood Thermo Fisher Cat# 221261 MethoCult M3134 Stem Cell Technologies Cat#03134 Iscove’s Modified Dulbecco’s Medium (IMDM) with 25mM HEPES Stem Cell Technologies Cat#361150 Anti-BSA Sigma-Aldrich Cat# B7276 Critical Commercial Assays RapiClear 1.55 Sunjin Lab Cat# RC155001 Zombie UV fixable viability kit Biolegend Cat# 423108 Arcturus PicoPure RNA isolation kit Thermo Fisher Cat# KIT0214 ERCC RNA Spike-In Mix Thermo Fisher Cat# 4456740 BrdU kit BD Biosciences Cat# 559619; RRID: AB_2617060 Deposited Data Raw RNA-seq data This Paper GEO: GSE109467 Experimental Models: Organisms/Strains Mouse: C57BL/6J The Jackson Laboratory Stock No: 000664 Mouse: Lyz2cre/cre: B6.129P2-Lyz2tm1(cre)Ifo/J The Jackson Laboratory Stock No: 004781 Mouse: S100a8cre: B6.Cg-Tg(S100A8-cre,-EGFP)1Ilw/J The Jackson Laboratory Stock No: 021614 Mouse: Rosa26mT/mG: STOCK Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J The Jackson Laboratory Stock No: 007676 Mouse: Cxcl12DsRed/+: STOCK Cxcl12tm2.1Sjm/J The Jackson Laboratory Stock No: 022458 Mouse: Rosa26LsL-YFP: B6.129X1-Gt(ROSA)26Sortm1(EYFP)Cos/J The Jackson Laboratory Stock No: 006148 Mouse: Albino B6: B6(Cg)-Tyrc-2J/J The Jackson Laboratory Stock No: 000104 Mouse: Cxcr4fl/fl: B6.129P2-Cxcr4tm2Yzo/J The Jackson Laboratory Stock No: 008767 (Continued on next page) e3 Immunity 48, 364–379.e1–e8, February 20, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse: Fucci-S/G2/M (#474) RIKEN BRC, Ibaraki, Japan Stock No: RBRC02704 Mouse: Fucci-G1 (#639) RIKEN BRC, Ibaraki, Japan Stock No: RBRC02709 Mouse: Lyz2gfp/+ (Lyz2tm1.1Graf) Thomas Graf, (Faust et al., 2000) N/A Mouse: Cxcr4WHIM (Cxcr41013/+) Françoise Bachelerie, (Balabanian et al., 2012) N/A Mouse: Cebpe / Philip H. Koeffler (Kyme et al., 2012) N/A Software and Algorithms Imaris Bitplane http://www.bitplane.com/imaris/imaris GraphPad Prism 7 GraphPad Software http://www.graphpad.com Cytofkit 1.6.5 Bioconductor https://bioconductor.org/packages/release/ bioc/html/cytofkit.html FlowJo 10 TreeStar http://flowjo.com/ FIJI (Fiji is just ImageJ) NIH http://imagej.nih.gov/ij Photoshop CS6 Adobe https://www.adobe.com/ t-SNE (van der Maaten and Hinton, 2008) https://cran.r-project.org/web/packages/ Rtsne/index.html MATLAB Mathworks https://www.mathworks.com/products/ matlab.html edgeR Bioconductor https://bioconductor.org/packages/ release/bioc/html/edgeR.html pheatmap R package https://cran.r-project.org/web/ packages/pheatmap/index.html Seriation (Hahsler et al., 2008) https://cran.r-project.org/web/packages/ seriation/index.html Enrichr (Chen et al., 2013) http://amp.pharm.mssm.edu/Enrichr/
Modification:Article Title: Developmental Analysis of Bone Marrow Neutrophils Reveals Populations Specialized in Expansion, Trafficking, and Effector Functions.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-human CD11b (Clone ICRF44) Biolegend Cat#301312; RRID: AB_314164 Anti-human CD16 (Clone 3G8) Fluidigm Cat#329002B Bacterial and Virus Strains DH5a Escherichia coli GFP (Chua and Wong, 2013) N/A Chemicals, Peptides, and Recombinant Proteins 1X RBC Lysis Buffer eBioscience Cat# 00-4333-57 5-Iodo-20-deoxyuridine (IdU) Sigma-Aldrich Cat# I7125 5–Fluorouracil Sigma-Aldrich Cat# F6627 Cisplatin Sigma-Aldrich Cat# 479306-1G CountBright Absolute Counting Beads Life Technologies Cat# C36950 DAPI Life Technologies Cat# D1306 Hema 3 Manual Staining System Thermo Fisher Cat# 22-122911 Dihydrorhodamine 123 Molecular Probes Cat# D23806 EQ Four Element Calibration Beads Fluidigm Cat# 201078 Human G-CSF (Neupogen) Amgen Cat# 100696800 Iridium Interchelator Fluidigm Cat# 201192B Dimethyl sulphoxide Sigma-Aldrich Cat# D5879 Paraformaldehyde Sigma-Aldrich Cat# 158127 Fixation/Permeabilization solution kit BD Bioscience Cat# 554714 Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat# P1585 Matrigel matrix growth factor reduced BD Bioscience Cat# 354230 Bovine Serum Albumin, lyophilized powder Sigma-Aldrich Cat# A2058 Evans Blue Sigma-Aldrich Cat# 46160 Trypticase Soy Agar (TSA II) with 5% Sheep Blood Thermo Fisher Cat# 221261 MethoCult M3134 Stem Cell Technologies Cat#03134 Iscove’s Modified Dulbecco’s Medium (IMDM) with 25mM HEPES Stem Cell Technologies Cat#361150 Anti-BSA Sigma-Aldrich Cat# B7276 Critical Commercial Assays RapiClear 1.55 Sunjin Lab Cat# RC155001 Zombie UV fixable viability kit Biolegend Cat# 423108 Arcturus PicoPure RNA isolation kit Thermo Fisher Cat# KIT0214 ERCC RNA Spike-In Mix Thermo Fisher Cat# 4456740 BrdU kit BD Biosciences Cat# 559619; RRID: AB_2617060 Deposited Data Raw RNA-seq data This Paper GEO: GSE109467 Experimental Models: Organisms/Strains Mouse: C57BL/6J The Jackson Laboratory Stock No: 000664 Mouse: Lyz2cre/cre: B6.129P2-Lyz2tm1(cre)Ifo/J The Jackson Laboratory Stock No: 004781 Mouse: S100a8cre: B6.Cg-Tg(S100A8-cre,-EGFP)1Ilw/J The Jackson Laboratory Stock No: 021614 Mouse: Rosa26mT/mG: STOCK Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J The Jackson Laboratory Stock No: 007676 Mouse: Cxcl12DsRed/+: STOCK Cxcl12tm2.1Sjm/J The Jackson Laboratory Stock No: 022458 Mouse: Rosa26LsL-YFP: B6.129X1-Gt(ROSA)26Sortm1(EYFP)Cos/J The Jackson Laboratory Stock No: 006148 Mouse: Albino B6: B6(Cg)-Tyrc-2J/J The Jackson Laboratory Stock No: 000104 Mouse: Cxcr4fl/fl: B6.129P2-Cxcr4tm2Yzo/J The Jackson Laboratory Stock No: 008767 (Continued on next page) e3 Immunity 48, 364–379.e1–e8, February 20, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse: Fucci-S/G2/M (#474) RIKEN BRC, Ibaraki, Japan Stock No: RBRC02704 Mouse: Fucci-G1 (#639) RIKEN BRC, Ibaraki, Japan Stock No: RBRC02709 Mouse: Lyz2gfp/+ (Lyz2tm1.1Graf) Thomas Graf, (Faust et al., 2000) N/A Mouse: Cxcr4WHIM (Cxcr41013/+) Françoise Bachelerie, (Balabanian et al., 2012) N/A Mouse: Cebpe / Philip H. Koeffler (Kyme et al., 2012) N/A Software and Algorithms Imaris Bitplane http://www.bitplane.com/imaris/imaris GraphPad Prism 7 GraphPad Software http://www.graphpad.com Cytofkit 1.6.5 Bioconductor https://bioconductor.org/packages/release/ bioc/html/cytofkit.html FlowJo 10 TreeStar http://flowjo.com/ FIJI (Fiji is just ImageJ) NIH http://imagej.nih.gov/ij Photoshop CS6 Adobe https://www.adobe.com/ t-SNE (van der Maaten and Hinton, 2008) https://cran.r-project.org/web/packages/ Rtsne/index.html MATLAB Mathworks https://www.mathworks.com/products/ matlab.html edgeR Bioconductor https://bioconductor.org/packages/ release/bioc/html/edgeR.html pheatmap R package https://cran.r-project.org/web/ packages/pheatmap/index.html Seriation (Hahsler et al., 2008) https://cran.r-project.org/web/packages/ seriation/index.html Enrichr (Chen et al., 2013) http://amp.pharm.mssm.edu/Enrichr/
Isolation:Article Title: Developmental Analysis of Bone Marrow Neutrophils Reveals Populations Specialized in Expansion, Trafficking, and Effector Functions.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-human CD11b (Clone ICRF44) Biolegend Cat#301312; RRID: AB_314164 Anti-human CD16 (Clone 3G8) Fluidigm Cat#329002B Bacterial and Virus Strains DH5a Escherichia coli GFP (Chua and Wong, 2013) N/A Chemicals, Peptides, and Recombinant Proteins 1X RBC Lysis Buffer eBioscience Cat# 00-4333-57 5-Iodo-20-deoxyuridine (IdU) Sigma-Aldrich Cat# I7125 5–Fluorouracil Sigma-Aldrich Cat# F6627 Cisplatin Sigma-Aldrich Cat# 479306-1G CountBright Absolute Counting Beads Life Technologies Cat# C36950 DAPI Life Technologies Cat# D1306 Hema 3 Manual Staining System Thermo Fisher Cat# 22-122911 Dihydrorhodamine 123 Molecular Probes Cat# D23806 EQ Four Element Calibration Beads Fluidigm Cat# 201078 Human G-CSF (Neupogen) Amgen Cat# 100696800 Iridium Interchelator Fluidigm Cat# 201192B Dimethyl sulphoxide Sigma-Aldrich Cat# D5879 Paraformaldehyde Sigma-Aldrich Cat# 158127 Fixation/Permeabilization solution kit BD Bioscience Cat# 554714 Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat# P1585 Matrigel matrix growth factor reduced BD Bioscience Cat# 354230 Bovine Serum Albumin, lyophilized powder Sigma-Aldrich Cat# A2058 Evans Blue Sigma-Aldrich Cat# 46160 Trypticase Soy Agar (TSA II) with 5% Sheep Blood Thermo Fisher Cat# 221261 MethoCult M3134 Stem Cell Technologies Cat#03134 Iscove’s Modified Dulbecco’s Medium (IMDM) with 25mM HEPES Stem Cell Technologies Cat#361150 Anti-BSA Sigma-Aldrich Cat# B7276 Critical Commercial Assays RapiClear 1.55 Sunjin Lab Cat# RC155001 Zombie UV fixable viability kit Biolegend Cat# 423108 Arcturus PicoPure RNA isolation kit Thermo Fisher Cat# KIT0214 ERCC RNA Spike-In Mix Thermo Fisher Cat# 4456740 BrdU kit BD Biosciences Cat# 559619; RRID: AB_2617060 Deposited Data Raw RNA-seq data This Paper GEO: GSE109467 Experimental Models: Organisms/Strains Mouse: C57BL/6J The Jackson Laboratory Stock No: 000664 Mouse: Lyz2cre/cre: B6.129P2-Lyz2tm1(cre)Ifo/J The Jackson Laboratory Stock No: 004781 Mouse: S100a8cre: B6.Cg-Tg(S100A8-cre,-EGFP)1Ilw/J The Jackson Laboratory Stock No: 021614 Mouse: Rosa26mT/mG: STOCK Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J The Jackson Laboratory Stock No: 007676 Mouse: Cxcl12DsRed/+: STOCK Cxcl12tm2.1Sjm/J The Jackson Laboratory Stock No: 022458 Mouse: Rosa26LsL-YFP: B6.129X1-Gt(ROSA)26Sortm1(EYFP)Cos/J The Jackson Laboratory Stock No: 006148 Mouse: Albino B6: B6(Cg)-Tyrc-2J/J The Jackson Laboratory Stock No: 000104 Mouse: Cxcr4fl/fl: B6.129P2-Cxcr4tm2Yzo/J The Jackson Laboratory Stock No: 008767 (Continued on next page) e3 Immunity 48, 364–379.e1–e8, February 20, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse: Fucci-S/G2/M (#474) RIKEN BRC, Ibaraki, Japan Stock No: RBRC02704 Mouse: Fucci-G1 (#639) RIKEN BRC, Ibaraki, Japan Stock No: RBRC02709 Mouse: Lyz2gfp/+ (Lyz2tm1.1Graf) Thomas Graf, (Faust et al., 2000) N/A Mouse: Cxcr4WHIM (Cxcr41013/+) Françoise Bachelerie, (Balabanian et al., 2012) N/A Mouse: Cebpe / Philip H. Koeffler (Kyme et al., 2012) N/A Software and Algorithms Imaris Bitplane http://www.bitplane.com/imaris/imaris GraphPad Prism 7 GraphPad Software http://www.graphpad.com Cytofkit 1.6.5 Bioconductor https://bioconductor.org/packages/release/ bioc/html/cytofkit.html FlowJo 10 TreeStar http://flowjo.com/ FIJI (Fiji is just ImageJ) NIH http://imagej.nih.gov/ij Photoshop CS6 Adobe https://www.adobe.com/ t-SNE (van der Maaten and Hinton, 2008) https://cran.r-project.org/web/packages/ Rtsne/index.html MATLAB Mathworks https://www.mathworks.com/products/ matlab.html edgeR Bioconductor https://bioconductor.org/packages/ release/bioc/html/edgeR.html pheatmap R package https://cran.r-project.org/web/ packages/pheatmap/index.html Seriation (Hahsler et al., 2008) https://cran.r-project.org/web/packages/ seriation/index.html Enrichr (Chen et al., 2013) http://amp.pharm.mssm.edu/Enrichr/
RNA Sequencing:Article Title: Developmental Analysis of Bone Marrow Neutrophils Reveals Populations Specialized in Expansion, Trafficking, and Effector Functions.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-human CD11b (Clone ICRF44) Biolegend Cat#301312; RRID: AB_314164 Anti-human CD16 (Clone 3G8) Fluidigm Cat#329002B Bacterial and Virus Strains DH5a Escherichia coli GFP (Chua and Wong, 2013) N/A Chemicals, Peptides, and Recombinant Proteins 1X RBC Lysis Buffer eBioscience Cat# 00-4333-57 5-Iodo-20-deoxyuridine (IdU) Sigma-Aldrich Cat# I7125 5–Fluorouracil Sigma-Aldrich Cat# F6627 Cisplatin Sigma-Aldrich Cat# 479306-1G CountBright Absolute Counting Beads Life Technologies Cat# C36950 DAPI Life Technologies Cat# D1306 Hema 3 Manual Staining System Thermo Fisher Cat# 22-122911 Dihydrorhodamine 123 Molecular Probes Cat# D23806 EQ Four Element Calibration Beads Fluidigm Cat# 201078 Human G-CSF (Neupogen) Amgen Cat# 100696800 Iridium Interchelator Fluidigm Cat# 201192B Dimethyl sulphoxide Sigma-Aldrich Cat# D5879 Paraformaldehyde Sigma-Aldrich Cat# 158127 Fixation/Permeabilization solution kit BD Bioscience Cat# 554714 Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat# P1585 Matrigel matrix growth factor reduced BD Bioscience Cat# 354230 Bovine Serum Albumin, lyophilized powder Sigma-Aldrich Cat# A2058 Evans Blue Sigma-Aldrich Cat# 46160 Trypticase Soy Agar (TSA II) with 5% Sheep Blood Thermo Fisher Cat# 221261 MethoCult M3134 Stem Cell Technologies Cat#03134 Iscove’s Modified Dulbecco’s Medium (IMDM) with 25mM HEPES Stem Cell Technologies Cat#361150 Anti-BSA Sigma-Aldrich Cat# B7276 Critical Commercial Assays RapiClear 1.55 Sunjin Lab Cat# RC155001 Zombie UV fixable viability kit Biolegend Cat# 423108 Arcturus PicoPure RNA isolation kit Thermo Fisher Cat# KIT0214 ERCC RNA Spike-In Mix Thermo Fisher Cat# 4456740 BrdU kit BD Biosciences Cat# 559619; RRID: AB_2617060 Deposited Data Raw RNA-seq data This Paper GEO: GSE109467 Experimental Models: Organisms/Strains Mouse: C57BL/6J The Jackson Laboratory Stock No: 000664 Mouse: Lyz2cre/cre: B6.129P2-Lyz2tm1(cre)Ifo/J The Jackson Laboratory Stock No: 004781 Mouse: S100a8cre: B6.Cg-Tg(S100A8-cre,-EGFP)1Ilw/J The Jackson Laboratory Stock No: 021614 Mouse: Rosa26mT/mG: STOCK Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J The Jackson Laboratory Stock No: 007676 Mouse: Cxcl12DsRed/+: STOCK Cxcl12tm2.1Sjm/J The Jackson Laboratory Stock No: 022458 Mouse: Rosa26LsL-YFP: B6.129X1-Gt(ROSA)26Sortm1(EYFP)Cos/J The Jackson Laboratory Stock No: 006148 Mouse: Albino B6: B6(Cg)-Tyrc-2J/J The Jackson Laboratory Stock No: 000104 Mouse: Cxcr4fl/fl: B6.129P2-Cxcr4tm2Yzo/J The Jackson Laboratory Stock No: 008767 (Continued on next page) e3 Immunity 48, 364–379.e1–e8, February 20, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse: Fucci-S/G2/M (#474) RIKEN BRC, Ibaraki, Japan Stock No: RBRC02704 Mouse: Fucci-G1 (#639) RIKEN BRC, Ibaraki, Japan Stock No: RBRC02709 Mouse: Lyz2gfp/+ (Lyz2tm1.1Graf) Thomas Graf, (Faust et al., 2000) N/A Mouse: Cxcr4WHIM (Cxcr41013/+) Françoise Bachelerie, (Balabanian et al., 2012) N/A Mouse: Cebpe / Philip H. Koeffler (Kyme et al., 2012) N/A Software and Algorithms Imaris Bitplane http://www.bitplane.com/imaris/imaris GraphPad Prism 7 GraphPad Software http://www.graphpad.com Cytofkit 1.6.5 Bioconductor https://bioconductor.org/packages/release/ bioc/html/cytofkit.html FlowJo 10 TreeStar http://flowjo.com/ FIJI (Fiji is just ImageJ) NIH http://imagej.nih.gov/ij Photoshop CS6 Adobe https://www.adobe.com/ t-SNE (van der Maaten and Hinton, 2008) https://cran.r-project.org/web/packages/ Rtsne/index.html MATLAB Mathworks https://www.mathworks.com/products/ matlab.html edgeR Bioconductor https://bioconductor.org/packages/ release/bioc/html/edgeR.html pheatmap R package https://cran.r-project.org/web/ packages/pheatmap/index.html Seriation (Hahsler et al., 2008) https://cran.r-project.org/web/packages/ seriation/index.html Enrichr (Chen et al., 2013) http://amp.pharm.mssm.edu/Enrichr/
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![Ability of chromium (III)-based compound to suppress colorectal cancer cells. A and B. MTT assay was used to determine the IC50 values of LoVoparental and LoVoOXAR colorectal cancer cell lines treated with the chromium (III)-based compound for 24 h. The IC50 values of LoVoparental and LoVoOXAR colorectal cancer cell lines were 500 and 2000 μg/mL, respectively. C. The two cell lines were compared. *P < 0.05, **P < 0.01, ***P < 0.001, and ****P < 0.0001 versus the control group of LoVoparental, and ##P < 0.01, and ####P < 0.0001 LoVoparental versus LoVoOXAR colorectal cancer cells. D. Clinical drugs were used as follows: oxaliplatin; 20 <t>µg/mL,</t> <t>5-FU;</t> 20 µg/mL, and irinotecan; 20 µg/mL. The synergetic effect of the chromium (III)-based compound when combined with clinical drugs significantly inhibited the viability of LoVoparental [200 μg/mL chromium (III)-based compound with 5 µg/mL oxaliplatin] and LoVoOXAR [500 μg/mL chromium (III)-based compound with 20 µg/mL oxaliplatin] colorectal cancer cell lines. The clinical drugs that inhibited the development of colorectal cancer cell lines were made more effective by the chromium (III)-based compound. Significance is denoted as *P < 0.05 and ***P < 0.001 versus the control group of LoVoparental cells, and #P < 0.05 and ###P < 0.001 versus the control group of LoVoOXAR cells. E-H. Epithelial-mesenchymal transition markers (E-cadherin and vimentin) were determined using immunofluorescence staining and western blot. GAPDH was used as an internal control. The scale bar was 50 μm. The data were expressed as mean ± standard deviation (SD, n = 3). *P < 0.05, **P < 0.01 versus control group.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_8745/pmc10998745/pmc10998745__ajcr0014-0979-f4.jpg)