Summary of Study ST003297
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002048. The data can be accessed directly via it's Project DOI: 10.21228/M8WG0S This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST003297 |
| Study Title | Metabolomic profiling of cultured TRAMP-C2 cells in the presence or absence of PD-L1. |
| Study Summary | Recent evidence suggests that PD-L1, well-known as the ligand of the immune inhibitory receptor PD-1, can have cell-intrinsic effects in cancer and immune cells. One such cell-intrinsic effect is modulation of cellular metabolism, including regulation of mTOR activity and glycolysis. Here, we analyzed the metabolome of cultured mouse prostate cancer cells (TRAMP-C2) expressing PD-L1 or with PD-L1 deleted via CRISPR/Cas9. |
| Institute | University of Ottawa |
| Last Name | Hodgins |
| First Name | Jonathan |
| Address | 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada |
| jonathanhodgins17@gmail.com | |
| Phone | 613-562-5800 |
| Submit Date | 2024-05-21 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-07-28 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002048 |
| Project DOI: | doi: 10.21228/M8WG0S |
| Project Title: | Metabolomic profiling of cultured TRAMP-C2 cells in the presence or absence of PD-L1. |
| Project Summary: | Recent evidence suggests that PD-L1, well-known as the ligand of the immune inhibitory receptor PD-1, can have cell-intrinsic effects in cancer and immune cells. One such cell-intrinsic effect is modulation of cellular metabolism, including regulation of mTOR activity and glycolysis. Here, we analyzed the metabolome of cultured mouse prostate cancer cells (TRAMP-C2) expressing PD-L1 or with PD-L1 deleted via CRISPR/Cas9. |
| Institute: | University of Ottawa |
| Last Name: | Hodgins |
| First Name: | Jonathan |
| Address: | 451 Smyth Rd, Ottawa, Ontario, K1H 8M5, Canada |
| Email: | jonathanhodgins17@gmail.com |
| Phone: | 613-562-5800 |
Subject:
| Subject ID: | SU003418 |
| Subject Type: | Cultured cells |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Gender: | Male |
| Cell Primary Immortalized: | Immortalized |
Factors:
Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Genotype |
|---|---|---|---|
| SA357986 | 2021-11-22 KO_Lys_1in100_06 | Cell lysate | PD-L1 KO |
| SA357987 | 2021-11-22 KO_Lys_1in10_02 | Cell lysate | PD-L1 KO |
| SA357988 | 2021-11-22 KO_Lys_UnDiluted_06 | Cell lysate | PD-L1 KO |
| SA357989 | 2021-11-22 KO_Lys_UnDiluted_05 | Cell lysate | PD-L1 KO |
| SA357990 | 2021-11-22 KO_Lys_UnDiluted_04 | Cell lysate | PD-L1 KO |
| SA357991 | 2021-11-22 KO_Lys_UnDiluted_03 | Cell lysate | PD-L1 KO |
| SA357992 | 2021-11-22 KO_Lys_UnDiluted_02 | Cell lysate | PD-L1 KO |
| SA357993 | 2021-11-22 KO_Lys_UnDiluted_01 | Cell lysate | PD-L1 KO |
| SA357994 | 2021-11-22 KO_Lys_1in10_01 | Cell lysate | PD-L1 KO |
| SA357995 | 2021-11-22 KO_Lys_1in100_05 | Cell lysate | PD-L1 KO |
| SA357996 | 2021-11-22 KO_Lys_1in10_05 | Cell lysate | PD-L1 KO |
| SA357997 | 2021-11-22 KO_Lys_1in10_03 | Cell lysate | PD-L1 KO |
| SA357998 | 2021-11-22 KO_Lys_1in10_04 | Cell lysate | PD-L1 KO |
| SA357999 | 2021-11-22 KO_Lys_1in100_04 | Cell lysate | PD-L1 KO |
| SA358000 | 2021-11-22 KO_Lys_1in10_06 | Cell lysate | PD-L1 KO |
| SA358001 | 2021-11-22 KO_Lys_1in100_01 | Cell lysate | PD-L1 KO |
| SA358002 | 2021-11-22 KO_Lys_1in100_02 | Cell lysate | PD-L1 KO |
| SA358003 | 2021-11-22 KO_Lys_1in100_03 | Cell lysate | PD-L1 KO |
| SA358004 | 2021-11-22 WT_Lys_1in100_05 | Cell lysate | Wild-type |
| SA358005 | 2021-11-22 WT_Lys_UnDiluted_06 | Cell lysate | Wild-type |
| SA358006 | 2021-11-22 WT_Lys_UnDiluted_05 | Cell lysate | Wild-type |
| SA358007 | 2021-11-22 WT_Lys_UnDiluted_04 | Cell lysate | Wild-type |
| SA358008 | 2021-11-22 WT_Lys_UnDiluted_03 | Cell lysate | Wild-type |
| SA358009 | 2021-11-22 WT_Lys_UnDiluted_02 | Cell lysate | Wild-type |
| SA358010 | 2021-11-22 WT_Lys_UnDiluted_01 | Cell lysate | Wild-type |
| SA358011 | 2021-11-22 WT_Lys_1in100_06 | Cell lysate | Wild-type |
| SA358012 | 2021-11-22 WT_Lys_1in100_04 | Cell lysate | Wild-type |
| SA358013 | 2021-11-22 WT_Lys_1in100_02 | Cell lysate | Wild-type |
| SA358014 | 2021-11-22 WT_Lys_1in100_01 | Cell lysate | Wild-type |
| SA358015 | 2021-11-22 WT_Lys_1in10_06 | Cell lysate | Wild-type |
| SA358016 | 2021-11-22 WT_Lys_1in10_05 | Cell lysate | Wild-type |
| SA358017 | 2021-11-22 WT_Lys_1in10_04 | Cell lysate | Wild-type |
| SA358018 | 2021-11-22 WT_Lys_1in10_03 | Cell lysate | Wild-type |
| SA358019 | 2021-11-22 WT_Lys_1in100_03 | Cell lysate | Wild-type |
| SA358020 | 2021-11-22 WT_Lys_1in10_01 | Cell lysate | Wild-type |
| SA358021 | 2021-11-22 WT_Lys_1in10_02 | Cell lysate | Wild-type |
| SA358022 | 2021-11-18 KO_Media_1in100_05 | Conditioned media | PD-L1 KO |
| SA358023 | 2021-11-24 KO_CM_UnDiluted_02 | Conditioned media | PD-L1 KO |
| SA358024 | 2021-11-24 KO_CM_UnDiluted_01 | Conditioned media | PD-L1 KO |
| SA358025 | 2021-11-24 KO_CM_UnDiluted_06 | Conditioned media | PD-L1 KO |
| SA358026 | 2021-11-24 KO_CM_UnDiluted_03 | Conditioned media | PD-L1 KO |
| SA358027 | 2021-11-24 KO_CM_UnDiluted_04 | Conditioned media | PD-L1 KO |
| SA358028 | 2021-11-24 KO_CM_UnDiluted_05 | Conditioned media | PD-L1 KO |
| SA358029 | 2021-11-18 KO_Media_1in100_06 | Conditioned media | PD-L1 KO |
| SA358030 | 2021-11-18 KO_Media_1in100_02 | Conditioned media | PD-L1 KO |
| SA358031 | 2021-11-18 KO_Media_1in100_04 | Conditioned media | PD-L1 KO |
| SA358032 | 2021-11-18 KO_Media_1in100_01 | Conditioned media | PD-L1 KO |
| SA358033 | 2021-11-18 KO_Media_1in10_01 | Conditioned media | PD-L1 KO |
| SA358034 | 2021-11-18 KO_Media_1in10_02 | Conditioned media | PD-L1 KO |
| SA358035 | 2021-11-18 KO_Media_1in10_04 | Conditioned media | PD-L1 KO |
| SA358036 | 2021-11-18 KO_Media_1in10_05 | Conditioned media | PD-L1 KO |
| SA358037 | 2021-11-18 KO_Media_1in100_03 | Conditioned media | PD-L1 KO |
| SA358038 | 2021-11-18 KO_Media_1in10_06 | Conditioned media | PD-L1 KO |
| SA358039 | 2021-11-18 KO_Media_1in10_03 | Conditioned media | PD-L1 KO |
| SA358040 | 2021-11-18 WT_Media_1in10_02 | Conditioned media | Wild-type |
| SA358041 | 2021-11-24 WT_CM_UnDiluted_06 | Conditioned media | Wild-type |
| SA358042 | 2021-11-24 WT_CM_UnDiluted_05 | Conditioned media | Wild-type |
| SA358043 | 2021-11-24 WT_CM_UnDiluted_04 | Conditioned media | Wild-type |
| SA358044 | 2021-11-24 WT_CM_UnDiluted_03 | Conditioned media | Wild-type |
| SA358045 | 2021-11-24 WT_CM_UnDiluted_02 | Conditioned media | Wild-type |
| SA358046 | 2021-11-24 WT_CM_UnDiluted_01 | Conditioned media | Wild-type |
| SA358047 | 2021-11-18 WT_Media_1in100_02 | Conditioned media | Wild-type |
| SA358048 | 2021-11-18 WT_Media_1in100_01 | Conditioned media | Wild-type |
| SA358049 | 2021-11-18 WT_Media_1in10_03 | Conditioned media | Wild-type |
| SA358050 | 2021-11-18 WT_Media_1in10_04 | Conditioned media | Wild-type |
| SA358051 | 2021-11-18 WT_Media_1in10_05 | Conditioned media | Wild-type |
| SA358052 | 2021-11-18 WT_Media_1in10_06 | Conditioned media | Wild-type |
| SA358053 | 2021-11-18 WT_Media_1in100_06 | Conditioned media | Wild-type |
| SA358054 | 2021-11-18 WT_Media_1in100_05 | Conditioned media | Wild-type |
| SA358055 | 2021-11-18 WT_Media_1in100_04 | Conditioned media | Wild-type |
| SA358056 | 2021-11-18 WT_Media_1in100_03 | Conditioned media | Wild-type |
| SA358057 | 2021-11-18 WT_Media_1in10_01 | Conditioned media | Wild-type |
| SA358058 | 2021-11-18 MediaOnly_1in10 | Culture media | N/A |
| SA358059 | 2021-11-18 MediaOnly_1in100. | Culture media | N/A |
| SA358060 | 2021-11-24 Media Only_UnDiluted | Culture media | N/A |
| Showing results 1 to 75 of 75 |
Collection:
| Collection ID: | CO003411 |
| Collection Summary: | Cells were placed on ice and the culture media was removed. Cells were washed twice with ice-cold PBS, and scraped into chilled 2 mL tubes, and frozen until metabolite extraction. |
| Sample Type: | Cultured cells |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003427 |
| Treatment Summary: | Cultured cells were not treated with any exogenous agents. |
Sample Preparation:
| Sampleprep ID: | SP003425 |
| Sampleprep Summary: | Samples were mixed with 230 uL of 1:1 methanol:water, along with 6 washed 1.4 mm ceramic beads. Samples were vortexed for 10 s and cell lysis was done by beating for 60 s at 2000 rpm (bead beating was done twice) after adding 220 µL of acetonitrile. Samples were then incubated with a 2:1 dichloromethane:water solution on ice for 10 minutes. The polar and non-polar phases were separated by centrifugation at 4000g for 10 minutes at 1°C. The upper polar phase was dried using a refrigerated CentriVap Vacuum Concentrator at -4°C (LabConco Corporation, Kansas City, MO). Samples were resuspended in water. |
| Processing Storage Conditions: | On ice |
Combined analysis:
| Analysis ID | AN005401 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 1290 Infinity II |
| Column | Agilent ZORBAX RRHD Extend-C18 (50 x 2.1mm,1.8um) |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Agilent 6470A |
| Ion Mode | NEGATIVE |
| Units | uM |
Chromatography:
| Chromatography ID: | CH004094 |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Agilent ZORBAX RRHD Extend-C18 (50 x 2.1mm,1.8um) |
| Column Temperature: | 35℃ |
| Flow Gradient: | 0-2.5 min 100% A, 2.5-7.5 min 100%-80% A; 7.5-13 min 80%-55% A, 13-20 min 55%-1% A, 20-24 min holding at 1% A, 24.05-31.5 min backflushing the column with 90% acetonitrile using channel C and then 32.25-40 min equilibrating the column with 100% A |
| Flow Rate: | 0.25 mL/min |
| Solvent A: | 100% Water; 10 mM tributylamine; 5 uM Agilent InfinityLab deactivator |
| Solvent B: | 100% Methanol; 10 mM tributylamine; 5 uM Agilent InfinityLab deactivator |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS005128 |
| Analysis ID: | AN005401 |
| Instrument Name: | Agilent 6470A |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Multiple reaction monitoring (MRM) transitions were optimized using authentic standards and quality control samples. Metabolites were quantified by integrating the area under the curve of each compound using external standard calibration curves with Mass Hunter Quant (Agilent). No corrections for ion suppression or enhancement were applied. |
| Ion Mode: | NEGATIVE |
