Return to study ST000584 main page
MB Sample ID: SA030985
Local Sample ID: | philic-30nov15-B004-r001 |
Subject ID: | SU000607 |
Subject Type: | Zebrafish |
Subject Species: | Danio rerio |
Taxonomy ID: | 7955 |
Species Group: | Fish |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU000607 |
Subject Type: | Zebrafish |
Subject Species: | Danio rerio |
Taxonomy ID: | 7955 |
Species Group: | Fish |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
philic-30nov15-B004-r001 | SA030985 | FL007170 | male | sex |
philic-30nov15-B004-r001 | SA030985 | FL007170 | brain | tissue |
philic-30nov15-B004-r001 | SA030985 | FL007170 | 24h post feeding | timepoint |
philic-30nov15-B004-r001 | SA030985 | FL007170 | WT | genotype |
Collection:
Collection ID: | CO000601 |
Collection Summary: | When testing the wildtype fasting fish, we only choose male fish. For each of the 3 time points, we scarifice 25 fish, put 5 tissue in one tube for 5 repeats. Because of tissue size, I adjusted heart sample at 2h and kidney sample at 2h to 3 repeats, liver sample at 2h to 4 repeats. For tfeb-/-fish, we collected heart, muscle, kidney with each of them 5 repeats. We collected both male and female. For lmna-/- we collected heart and muscle(only male) with each 3 repeats. |
Sample Type: | Blood |
Treatment:
Treatment ID: | TR000621 |
Treatment Summary: | This is pre-test study for protocal development and baseline measures. Fish hearts are small, and more than 30 adult fish heart might need to be pooled to generated sufficient sample for a metabolic profiling experiments. Therefore, we will first test the condition using wild type fish at 3 months for this purpose. Tfeb -/- knockouts and lmna -/- knockouts are similarily being used for protocal development. After we optimize the protocol, we will assess changes in DOX-induced cardiomyopathy. |
Sample Preparation:
Sampleprep ID: | SP000614 |
Sampleprep Summary: | Handling of tissue 1) Keep tubes on ice for 10 min. Spin down @ 1000 RCF for 30 sec 2) Add 20 ul PBS per sample and 3 ul 13C6-Phe 3) Sonicate on ice bath for 30 sec x 4 times 4) Add 250 ul ACN/MeOH mixture and incubate on ice for 30 min 5) Pool 20 ul sup from each sample and split 100 ul pool in 5 tubes 6) Split remaining sup in two 1 dram vials x 2 (100 ul per vial) 7) Dry under N2 stream |
Combined analysis:
Analysis ID | AN000896 | AN000897 | AN000898 | AN000899 |
---|---|---|---|---|
Analysis type | MS | MS | MS | MS |
Chromatography type | HILIC | HILIC | Reversed phase | Reversed phase |
Chromatography system | Agilent 1290 Infinity | Agilent 1290 Infinity | Agilent 1290 Infinity | Agilent 1290 Infinity |
Column | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) | Waters Acquity HSS C18 (150 x 2.1mm,1.8um) | Waters Acquity HSS C18 (150 x 2.1mm,1.8um) |
MS Type | ESI | ESI | ESI | ESI |
MS instrument type | QTOF | QTOF | QTOF | QTOF |
MS instrument name | Agilent 6550 QTOF | Agilent 6550 QTOF | Agilent 6550 QTOF | Agilent 6550 QTOF |
Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
Units | unspecified | unspecified | unspecified | unspecified |
Chromatography:
Chromatography ID: | CH000638 |
Instrument Name: | Agilent 1290 Infinity |
Column Name: | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
Chromatography Type: | HILIC |
Chromatography ID: | CH000639 |
Instrument Name: | Agilent 1290 Infinity |
Column Name: | Waters Acquity HSS C18 (150 x 2.1mm,1.8um) |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS000798 |
Analysis ID: | AN000896 |
Instrument Name: | Agilent 6550 QTOF |
Instrument Type: | QTOF |
MS Type: | ESI |
Ion Mode: | POSITIVE |
MS ID: | MS000799 |
Analysis ID: | AN000897 |
Instrument Name: | Agilent 6550 QTOF |
Instrument Type: | QTOF |
MS Type: | ESI |
Ion Mode: | NEGATIVE |
MS ID: | MS000800 |
Analysis ID: | AN000898 |
Instrument Name: | Agilent 6550 QTOF |
Instrument Type: | QTOF |
MS Type: | ESI |
Ion Mode: | POSITIVE |
MS ID: | MS000801 |
Analysis ID: | AN000899 |
Instrument Name: | Agilent 6550 QTOF |
Instrument Type: | QTOF |
MS Type: | ESI |
Ion Mode: | NEGATIVE |