Biomarker Discovery:Article Title: Proteogenomic characterization of non-functional pancreatic neuroendocrine tumors unravels clinically relevant subgroups.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti- TIM3 Cell Signaling Technology Cat# 45208;RRID: AB_2797623 Anti- CD163 proteintech Cat# 18942-1-AP;RRID: AB_2877129 Anti- CD39 Abcam Cat# Ab223842;RRID: AB_2892627 Anti- CD68 Cell Signaling Technology Cat# 97778;RRID: AB_2797703 Anti- TGF-b1 Abcam Cat# Ab215715;RRID: AB_2892628 Anti- TGF-b3 Abcam Cat# Ab15537; RRID: AB_443060 Anti- SLC3A2 Abclonal Cat# A19880; RRID: AB_2923508 Anti- P4HA1 Abclonal Cat# A10538; RRID: AB_2923507 Anti- PFKP Abclonal Cat# A20983; RRID: AB_2923508 Anti- Synaptopodin proteintech Cat# 21064-1-AP; RRID: AB_2877130 Anti- PCPE-1 Santa Crue Cat# SC73002; RRID: AB_1122044 Anti- BMERB1 Thermofisher Cat# PA5-148273; RRID: AB_2923509 Anti- GNAO1 Abcam Cat# Ab259884; RRID: AB_2923510 Anti- INA Abclonal Cat# A3596; RRID: AB_2923511 Anti- VCAN Abcam Cat# Ab270445; RRID: AB_2923512 Anti- CDK5 Proteintech Cat# 10430-1-AP; RRID: AB_2877131 Anti- CACNA1D Proteintech Cat# 22276-1-AP; RRID: AB_2877132 Anti- CD8 Proteintech Cat# 66868-1-Ig; RRID: AB_2923513 Anti- CD3 Proteintech Cat# 17617-1-AP; RRID: AB_2877133 Anti- Granzyme B Proteintech Cat# 13588-1-AP;RRID: AB_2877134 Anti- Ki67 Proteintech Cat# 27309-1-AP; RRID: AB_2877135 Biological samples Paired tumor and normal adjacent tissues from 108 NF-PanNET patients (discovery cohort) Fudan University Shanghai Cancer Center Table S1A Tumor tissues of 51 NF-PanNET patients (validation cohort) Fudan University Shanghai Cancer Center Table S1B FFPE samples of an independent cohort of 79 tumors Fudan University Shanghai Cancer Center Table S1C FFPE samples of an independent external cohort of 88 tumors Shanghai Changhai Hospital This paper Tumor tissues from 13 gastrointestinal NET patients Fudan University Shanghai Cancer Center This paper Peripheral blood samples from 79 healthy individuals and an independent cohort of 108 NF-PanNET patients Fudan University Shanghai Cancer Center This paper Patient-derived xenografts (PDXs) Fudan University Shanghai Cancer Center Table S7B Chemicals, peptides, and recombinant proteins LC-MS grade water Fisher chemical Cat# W6-4 LC-MS grade Acetonitrile Fisher chemical Cat# A955-4 LC-MS grade methanol Merck Cat# 1.06007 LC-MS grade Ethanol Merck Cat# 1.11727 Sodium dodecyl sulfate Sigma Cat# L4509 Formic acid Sigma Cat# 5330020050 (Continued on next page) e1 Cancer Cell 43, 1–21.e1–e14, April 14, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tris VWR Life Science Cat# 0497 Urea Sigma Cat# U5128 Dithiothretiol Sigma Cat# D9163 Iodoacetamide Sigma Cat# I1149 Sequencing-grade modified trypsin Promega Cat# V5111 Trifluoroacetic acid Sigma Cat# 302031 50% Hydroxylamine Thermo Fisher Scientific Cat# 90115 Ammonium formate Fluka Cat# 70221 Ammonium bicarbonate Sigma Cat# A6141 Triethylammonium bicarbonate Sigma Cat# T7408 Ammonium hydroxide Sigma Cat# 30501 Reversed-phase tC18 SepPak Waters Cat# WAT036790 Tris(2-carboxyethyl) phosphine hydrochloride Sigma Cat# 75259-1G Chloroacetamide Sigma Cat# 22790-250G-F Tryptophan Sigma Cat# T0254 ReproSil-Pur, 120 Å, C18-AQ, 1.9-mm resin Dr. Maisch Cat# r119.aq.
Formalin-fixed Paraffin-Embedded:Article Title: Proteogenomic characterization of non-functional pancreatic neuroendocrine tumors unravels clinically relevant subgroups.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti- TIM3 Cell Signaling Technology Cat# 45208;RRID: AB_2797623 Anti- CD163 proteintech Cat# 18942-1-AP;RRID: AB_2877129 Anti- CD39 Abcam Cat# Ab223842;RRID: AB_2892627 Anti- CD68 Cell Signaling Technology Cat# 97778;RRID: AB_2797703 Anti- TGF-b1 Abcam Cat# Ab215715;RRID: AB_2892628 Anti- TGF-b3 Abcam Cat# Ab15537; RRID: AB_443060 Anti- SLC3A2 Abclonal Cat# A19880; RRID: AB_2923508 Anti- P4HA1 Abclonal Cat# A10538; RRID: AB_2923507 Anti- PFKP Abclonal Cat# A20983; RRID: AB_2923508 Anti- Synaptopodin proteintech Cat# 21064-1-AP; RRID: AB_2877130 Anti- PCPE-1 Santa Crue Cat# SC73002; RRID: AB_1122044 Anti- BMERB1 Thermofisher Cat# PA5-148273; RRID: AB_2923509 Anti- GNAO1 Abcam Cat# Ab259884; RRID: AB_2923510 Anti- INA Abclonal Cat# A3596; RRID: AB_2923511 Anti- VCAN Abcam Cat# Ab270445; RRID: AB_2923512 Anti- CDK5 Proteintech Cat# 10430-1-AP; RRID: AB_2877131 Anti- CACNA1D Proteintech Cat# 22276-1-AP; RRID: AB_2877132 Anti- CD8 Proteintech Cat# 66868-1-Ig; RRID: AB_2923513 Anti- CD3 Proteintech Cat# 17617-1-AP; RRID: AB_2877133 Anti- Granzyme B Proteintech Cat# 13588-1-AP;RRID: AB_2877134 Anti- Ki67 Proteintech Cat# 27309-1-AP; RRID: AB_2877135 Biological samples Paired tumor and normal adjacent tissues from 108 NF-PanNET patients (discovery cohort) Fudan University Shanghai Cancer Center Table S1A Tumor tissues of 51 NF-PanNET patients (validation cohort) Fudan University Shanghai Cancer Center Table S1B FFPE samples of an independent cohort of 79 tumors Fudan University Shanghai Cancer Center Table S1C FFPE samples of an independent external cohort of 88 tumors Shanghai Changhai Hospital This paper Tumor tissues from 13 gastrointestinal NET patients Fudan University Shanghai Cancer Center This paper Peripheral blood samples from 79 healthy individuals and an independent cohort of 108 NF-PanNET patients Fudan University Shanghai Cancer Center This paper Patient-derived xenografts (PDXs) Fudan University Shanghai Cancer Center Table S7B Chemicals, peptides, and recombinant proteins LC-MS grade water Fisher chemical Cat# W6-4 LC-MS grade Acetonitrile Fisher chemical Cat# A955-4 LC-MS grade methanol Merck Cat# 1.06007 LC-MS grade Ethanol Merck Cat# 1.11727 Sodium dodecyl sulfate Sigma Cat# L4509 Formic acid Sigma Cat# 5330020050 (Continued on next page) e1 Cancer Cell 43, 1–21.e1–e14, April 14, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tris VWR Life Science Cat# 0497 Urea Sigma Cat# U5128 Dithiothretiol Sigma Cat# D9163 Iodoacetamide Sigma Cat# I1149 Sequencing-grade modified trypsin Promega Cat# V5111 Trifluoroacetic acid Sigma Cat# 302031 50% Hydroxylamine Thermo Fisher Scientific Cat# 90115 Ammonium formate Fluka Cat# 70221 Ammonium bicarbonate Sigma Cat# A6141 Triethylammonium bicarbonate Sigma Cat# T7408 Ammonium hydroxide Sigma Cat# 30501 Reversed-phase tC18 SepPak Waters Cat# WAT036790 Tris(2-carboxyethyl) phosphine hydrochloride Sigma Cat# 75259-1G Chloroacetamide Sigma Cat# 22790-250G-F Tryptophan Sigma Cat# T0254 ReproSil-Pur, 120 Å, C18-AQ, 1.9-mm resin Dr. Maisch Cat# r119.aq.
Recombinant:Article Title: Proteogenomic characterization of non-functional pancreatic neuroendocrine tumors unravels clinically relevant subgroups.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti- TIM3 Cell Signaling Technology Cat# 45208;RRID: AB_2797623 Anti- CD163 proteintech Cat# 18942-1-AP;RRID: AB_2877129 Anti- CD39 Abcam Cat# Ab223842;RRID: AB_2892627 Anti- CD68 Cell Signaling Technology Cat# 97778;RRID: AB_2797703 Anti- TGF-b1 Abcam Cat# Ab215715;RRID: AB_2892628 Anti- TGF-b3 Abcam Cat# Ab15537; RRID: AB_443060 Anti- SLC3A2 Abclonal Cat# A19880; RRID: AB_2923508 Anti- P4HA1 Abclonal Cat# A10538; RRID: AB_2923507 Anti- PFKP Abclonal Cat# A20983; RRID: AB_2923508 Anti- Synaptopodin proteintech Cat# 21064-1-AP; RRID: AB_2877130 Anti- PCPE-1 Santa Crue Cat# SC73002; RRID: AB_1122044 Anti- BMERB1 Thermofisher Cat# PA5-148273; RRID: AB_2923509 Anti- GNAO1 Abcam Cat# Ab259884; RRID: AB_2923510 Anti- INA Abclonal Cat# A3596; RRID: AB_2923511 Anti- VCAN Abcam Cat# Ab270445; RRID: AB_2923512 Anti- CDK5 Proteintech Cat# 10430-1-AP; RRID: AB_2877131 Anti- CACNA1D Proteintech Cat# 22276-1-AP; RRID: AB_2877132 Anti- CD8 Proteintech Cat# 66868-1-Ig; RRID: AB_2923513 Anti- CD3 Proteintech Cat# 17617-1-AP; RRID: AB_2877133 Anti- Granzyme B Proteintech Cat# 13588-1-AP;RRID: AB_2877134 Anti- Ki67 Proteintech Cat# 27309-1-AP; RRID: AB_2877135 Biological samples Paired tumor and normal adjacent tissues from 108 NF-PanNET patients (discovery cohort) Fudan University Shanghai Cancer Center Table S1A Tumor tissues of 51 NF-PanNET patients (validation cohort) Fudan University Shanghai Cancer Center Table S1B FFPE samples of an independent cohort of 79 tumors Fudan University Shanghai Cancer Center Table S1C FFPE samples of an independent external cohort of 88 tumors Shanghai Changhai Hospital This paper Tumor tissues from 13 gastrointestinal NET patients Fudan University Shanghai Cancer Center This paper Peripheral blood samples from 79 healthy individuals and an independent cohort of 108 NF-PanNET patients Fudan University Shanghai Cancer Center This paper Patient-derived xenografts (PDXs) Fudan University Shanghai Cancer Center Table S7B Chemicals, peptides, and recombinant proteins LC-MS grade water Fisher chemical Cat# W6-4 LC-MS grade Acetonitrile Fisher chemical Cat# A955-4 LC-MS grade methanol Merck Cat# 1.06007 LC-MS grade Ethanol Merck Cat# 1.11727 Sodium dodecyl sulfate Sigma Cat# L4509 Formic acid Sigma Cat# 5330020050 (Continued on next page) e1 Cancer Cell 43, 1–21.e1–e14, April 14, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tris VWR Life Science Cat# 0497 Urea Sigma Cat# U5128 Dithiothretiol Sigma Cat# D9163 Iodoacetamide Sigma Cat# I1149 Sequencing-grade modified trypsin Promega Cat# V5111 Trifluoroacetic acid Sigma Cat# 302031 50% Hydroxylamine Thermo Fisher Scientific Cat# 90115 Ammonium formate Fluka Cat# 70221 Ammonium bicarbonate Sigma Cat# A6141 Triethylammonium bicarbonate Sigma Cat# T7408 Ammonium hydroxide Sigma Cat# 30501 Reversed-phase tC18 SepPak Waters Cat# WAT036790 Tris(2-carboxyethyl) phosphine hydrochloride Sigma Cat# 75259-1G Chloroacetamide Sigma Cat# 22790-250G-F Tryptophan Sigma Cat# T0254 ReproSil-Pur, 120 Å, C18-AQ, 1.9-mm resin Dr. Maisch Cat# r119.aq.
Liquid Chromatography with Mass Spectroscopy:Article Title: Proteogenomic characterization of non-functional pancreatic neuroendocrine tumors unravels clinically relevant subgroups.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti- TIM3 Cell Signaling Technology Cat# 45208;RRID: AB_2797623 Anti- CD163 proteintech Cat# 18942-1-AP;RRID: AB_2877129 Anti- CD39 Abcam Cat# Ab223842;RRID: AB_2892627 Anti- CD68 Cell Signaling Technology Cat# 97778;RRID: AB_2797703 Anti- TGF-b1 Abcam Cat# Ab215715;RRID: AB_2892628 Anti- TGF-b3 Abcam Cat# Ab15537; RRID: AB_443060 Anti- SLC3A2 Abclonal Cat# A19880; RRID: AB_2923508 Anti- P4HA1 Abclonal Cat# A10538; RRID: AB_2923507 Anti- PFKP Abclonal Cat# A20983; RRID: AB_2923508 Anti- Synaptopodin proteintech Cat# 21064-1-AP; RRID: AB_2877130 Anti- PCPE-1 Santa Crue Cat# SC73002; RRID: AB_1122044 Anti- BMERB1 Thermofisher Cat# PA5-148273; RRID: AB_2923509 Anti- GNAO1 Abcam Cat# Ab259884; RRID: AB_2923510 Anti- INA Abclonal Cat# A3596; RRID: AB_2923511 Anti- VCAN Abcam Cat# Ab270445; RRID: AB_2923512 Anti- CDK5 Proteintech Cat# 10430-1-AP; RRID: AB_2877131 Anti- CACNA1D Proteintech Cat# 22276-1-AP; RRID: AB_2877132 Anti- CD8 Proteintech Cat# 66868-1-Ig; RRID: AB_2923513 Anti- CD3 Proteintech Cat# 17617-1-AP; RRID: AB_2877133 Anti- Granzyme B Proteintech Cat# 13588-1-AP;RRID: AB_2877134 Anti- Ki67 Proteintech Cat# 27309-1-AP; RRID: AB_2877135 Biological samples Paired tumor and normal adjacent tissues from 108 NF-PanNET patients (discovery cohort) Fudan University Shanghai Cancer Center Table S1A Tumor tissues of 51 NF-PanNET patients (validation cohort) Fudan University Shanghai Cancer Center Table S1B FFPE samples of an independent cohort of 79 tumors Fudan University Shanghai Cancer Center Table S1C FFPE samples of an independent external cohort of 88 tumors Shanghai Changhai Hospital This paper Tumor tissues from 13 gastrointestinal NET patients Fudan University Shanghai Cancer Center This paper Peripheral blood samples from 79 healthy individuals and an independent cohort of 108 NF-PanNET patients Fudan University Shanghai Cancer Center This paper Patient-derived xenografts (PDXs) Fudan University Shanghai Cancer Center Table S7B Chemicals, peptides, and recombinant proteins LC-MS grade water Fisher chemical Cat# W6-4 LC-MS grade Acetonitrile Fisher chemical Cat# A955-4 LC-MS grade methanol Merck Cat# 1.06007 LC-MS grade Ethanol Merck Cat# 1.11727 Sodium dodecyl sulfate Sigma Cat# L4509 Formic acid Sigma Cat# 5330020050 (Continued on next page) e1 Cancer Cell 43, 1–21.e1–e14, April 14, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tris VWR Life Science Cat# 0497 Urea Sigma Cat# U5128 Dithiothretiol Sigma Cat# D9163 Iodoacetamide Sigma Cat# I1149 Sequencing-grade modified trypsin Promega Cat# V5111 Trifluoroacetic acid Sigma Cat# 302031 50% Hydroxylamine Thermo Fisher Scientific Cat# 90115 Ammonium formate Fluka Cat# 70221 Ammonium bicarbonate Sigma Cat# A6141 Triethylammonium bicarbonate Sigma Cat# T7408 Ammonium hydroxide Sigma Cat# 30501 Reversed-phase tC18 SepPak Waters Cat# WAT036790 Tris(2-carboxyethyl) phosphine hydrochloride Sigma Cat# 75259-1G Chloroacetamide Sigma Cat# 22790-250G-F Tryptophan Sigma Cat# T0254 ReproSil-Pur, 120 Å, C18-AQ, 1.9-mm resin Dr. Maisch Cat# r119.aq.
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