Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA170661

Local Sample ID:	M2b_037_081418
Subject ID:	SU001912
Subject Type:	Human
Subject Species:	Homo sapiens
Taxonomy ID:	9606

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Sample Preparation:

Sampleprep ID:	SP001918
Sampleprep Summary:	With the goal of creating a comprehensive snapshot of cellular function, multiple experimental sample types were collected from each MΦ phenotype during cell harvest to obtain transcriptomic, proteomic, and metabolomic data from each experimental trial. At the desired time point, the cellular supernatant, composed of cell culture media and any non-adherent cells, was removed from the cell culture well and placed into falcon tubes on ice. One mL of ice-cold phosphate buffered saline (PBS) was added to the adherent cell layers and then removed to the tubes containing the cellular supernatant and the tubes centrifuged at 2000 rpm for 8 minutes. The collected supernatant was stored at -80° C until further analysis. Pelleted cells were flash-frozen in liquid nitrogen and stored on ice, while the remaining adherent cells were quenched with 350 µL of ice-cold 100% methanol (Honeywell; Muskegon, MI, USA) and 350 µL of ice-cold ultrapure distilled water (Invitrogen; Grand Island NY, USA) and removed through gentle cell scraping and added to the cell pellet fraction. Following the addition of 700 µL of ice-cold chloroform (Acros Organics; Thermo Fisher Scientific; Waltham, MA, USA), the collected cells were vortexed for 30 seconds and were transferred to FastPrep® lysing matrix D tubes (MP Biomedicals; Auckland, New Zealand). To achieve cell lysis, the tubes were homogenized during two cycles of 40 s each at 4.0 m/s with a 90 s delay between cycles utilizing the FastPrep-24™ 5G Homogenizer (MP Biomedicals; Auckland, New Zealand). The homogenized samples were centrifuged at 16,000 x g for 5 minutes at 4° C, and then placed immediately on ice. The polar (methanol/water) layer and non-polar (chloroform) layers were subsequently transferred to 1.5 mL protein low binding microcentrifuge tubes. These metabolite suspensions were lyophilized overnight without heat on a Thermo Scientific™ Savant™ ISS110 SpeedVac™ (Waltham, MA, USA) and stored at -80°C until the samples were shipped to Metabolon for further analysis. The remaining interphase layer was flash-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

Sampleprep ID:

SP001918

Sampleprep Summary:

With the goal of creating a comprehensive snapshot of cellular function, multiple experimental sample types were collected from each MΦ phenotype during cell harvest to obtain transcriptomic, proteomic, and metabolomic data from each experimental trial. At the desired time point, the cellular supernatant, composed of cell culture media and any non-adherent cells, was removed from the cell culture well and placed into falcon tubes on ice. One mL of ice-cold phosphate buffered saline (PBS) was added to the adherent cell layers and then removed to the tubes containing the cellular supernatant and the tubes centrifuged at 2000 rpm for 8 minutes. The collected supernatant was stored at -80° C until further analysis. Pelleted cells were flash-frozen in liquid nitrogen and stored on ice, while the remaining adherent cells were quenched with 350 µL of ice-cold 100% methanol (Honeywell; Muskegon, MI, USA) and 350 µL of ice-cold ultrapure distilled water (Invitrogen; Grand Island NY, USA) and removed through gentle cell scraping and added to the cell pellet fraction. Following the addition of 700 µL of ice-cold chloroform (Acros Organics; Thermo Fisher Scientific; Waltham, MA, USA), the collected cells were vortexed for 30 seconds and were transferred to FastPrep® lysing matrix D tubes (MP Biomedicals; Auckland, New Zealand). To achieve cell lysis, the tubes were homogenized during two cycles of 40 s each at 4.0 m/s with a 90 s delay between cycles utilizing the FastPrep-24™ 5G Homogenizer (MP Biomedicals; Auckland, New Zealand). The homogenized samples were centrifuged at 16,000 x g for 5 minutes at 4° C, and then placed immediately on ice. The polar (methanol/water) layer and non-polar (chloroform) layers were subsequently transferred to 1.5 mL protein low binding microcentrifuge tubes. These metabolite suspensions were lyophilized overnight without heat on a Thermo Scientific™ Savant™ ISS110 SpeedVac™ (Waltham, MA, USA) and stored at -80°C until the samples were shipped to Metabolon for further analysis. The remaining interphase layer was flash-frozen in liquid nitrogen and stored at -80°C until RNA extraction.