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MB Sample ID: SA301597
| Local Sample ID: | MUSC-00307 |
| Subject ID: | SU002916 |
| Subject Type: | Mammal |
| Subject Species: | Mouse/canine |
| Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002916 |
| Subject Type: | Mammal |
| Subject Species: | Mouse/canine |
| Taxonomy ID: | 9606 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| MUSC-00307 | SA301597 | FL036605 | IFT88_KO_WT | Genotype |
Collection:
| Collection ID: | CO002909 |
| Collection Summary: | Six independent replicates of Exoc5 OE, KD, CTS-mut, and control MDCK cells were grown in cell culture in 15 cm dishes. The cells were then washed in PBS, scraped, and centrifuged to a pellet and snap frozen in liquid nitrogen. Similarly six independent replicates of murine Ift88 KO and rescue cells were grown in cell culture, washed with PBS, scraped, centrifuged to a pellet and snap frozen in liquid nitrogen. |
| Sample Type: | Cultured kidney cells |
Treatment:
| Treatment ID: | TR002925 |
| Treatment Summary: | No treatment |
Sample Preparation:
| Sampleprep ID: | SP002922 |
| Sampleprep Summary: | Samples were thawed on ice prior to extraction. Samples were prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards were added prior to the first step in the extraction process for QC purposes. In order to dissociate small molecules bound to or trapped in proteins, lysate was precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation. The resulting extract was divided into multiple fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS with negative ion mode ESI, and remaining fractions reserved for backup. Samples were dried under warm nitrogen to remove the organic solvent. The sample extracts were stored sealed at -80oC if not analyzed immediately. |
Combined analysis:
| Analysis ID | AN004566 | AN004567 | AN004568 | AN004569 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | Reversed phase | HILIC |
| Chromatography system | Waters Acquity | Waters Acquity | Waters Acquity | Waters Acquity |
| Column | Waters Acquity BEH C18 (100 x 2mm, 1.7um) | Waters Acquity BEH C18 (100 x 2mm, 1.7um) | Waters Acquity BEH C18 (100 x 2mm, 1.7um) | Waters Acquity BEH Amide (150 x 2.1mm, 1.7um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE | NEGATIVE |
| Units | Normalized/scaled raw area counts | Normalized/scaled raw area counts | Normalized/scaled raw area counts | Normalized/scaled raw area counts |
Chromatography:
| Chromatography ID: | CH003431 |
| Chromatography Summary: | Low pH polar |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 1.7um) |
| Column Temperature: | 65 |
| Flow Gradient: | Linear gradient from 5% B to 80% B over 3.35 minutes. |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 0.1% formic acid and 0.05% PFPA in water, pH ~2.5 |
| Solvent B: | 0.1% formic acid and 0.05% PFPA in methanol, pH ~2.5 |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003432 |
| Chromatography Summary: | Low pH Lipophilic |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 1.7um) |
| Column Temperature: | 65 |
| Flow Gradient: | Linear gradient from 40 % B to 99.5% B over 1.0 minute, hold 99.5% B for 2.4 minutes |
| Flow Rate: | 0.60 mL/min |
| Solvent A: | 0.1% formic acid and 0.05% PFPA in water, pH ~2.5 |
| Solvent B: | 0.1% formic acid and 0.05% PFPA in 50% methanol/ 50% acetonitrile, pH ~2.5 |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003433 |
| Chromatography Summary: | High pH |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 1.7um) |
| Column Temperature: | 65 |
| Flow Gradient: | Linear gradient from 0.5 to 70% B over 4.0 minutes, then rapid gradient to 99%B in 0.5 minutes. |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 6.5 mM ammonium bicarbonate in water, pH 8 |
| Solvent B: | 6.5 mM ammonium bicarbonate in 95% methanol/ 5% water |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003434 |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH Amide (150 x 2.1mm, 1.7um) |
| Column Temperature: | 65 |
| Flow Gradient: | Linear gradient from 5% B to 50% B in 3.5 minutes, then linear gradient from 50% B to 95% B in 2 minutes minutes. |
| Flow Rate: | 0.50 mL/min |
| Solvent A: | 10 mM ammonium formate in 15% water/ 5% methanol/ 80% acetonitrile (effective pH 10.16 with NH4OH) |
| Solvent B: | 10 mM ammonium formate in 50% water/ 50% acetonitrile (effective pH 10.60 with NH4OH) |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS004312 |
| Analysis ID: | AN004566 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Proprietary analytical software for integration and peak picking (Metabolon). Normalized raw area counts for each sample are normalized by Bradford protein concentration. Each metabolite is then rescaled to set the median equal to 1. Lastly, missing values are imputed with the minimum. |
| Ion Mode: | POSITIVE |
| MS ID: | MS004313 |
| Analysis ID: | AN004567 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Proprietary analytical software for integration and peak picking (Metabolon). Normalized raw area counts for each sample are normalized by Bradford protein concentration. Each metabolite is then rescaled to set the median equal to 1. Lastly, missing values are imputed with the minimum. |
| Ion Mode: | POSITIVE |
| MS ID: | MS004314 |
| Analysis ID: | AN004568 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Proprietary analytical software for integration and peak picking (Metabolon). Normalized raw area counts for each sample are normalized by Bradford protein concentration. Each metabolite is then rescaled to set the median equal to 1. Lastly, missing values are imputed with the minimum. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS004315 |
| Analysis ID: | AN004569 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Proprietary analytical software for integration and peak picking (Metabolon). Normalized raw area counts for each sample are normalized by Bradford protein concentration. E.ach metabolite is then rescaled to set the median equal to 1. Lastly, missing values are imputed with the minimum. |
| Ion Mode: | NEGATIVE |
