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MB Sample ID: SA125940
Local Sample ID: | SC_20190605_RPLCp_FMS_Embryo_S15 |
Subject ID: | SU001568 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU001568 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
SC_20190605_RPLCp_FMS_Embryo_S15 | SA125940 | FL015461 | Embryo culture media_device | Device |
Collection:
Collection ID: | CO001563 |
Collection Summary: | Samples were collected from microdrops and microfluidic devices when embryos developed to fully expanded blastocyst stage, to allow stage-matched comparison of embryo metabolite production/consumption. |
Sample Type: | Blastocysts |
Treatment:
Treatment ID: | TR001583 |
Treatment Summary: | Control KSOM: fresh medium at day 0 not incubated in devices or microdrops. Day 4 KSOM_drop: medium incubated in microdrops for 4 days without embryos Day 5 KSOM_device: medium incubated in devices for 5 days without embryos Day 4 KSOM_drop_embryos: medium incubated in microdrops for 4 days with embryos Day 5 KSOM_device_embryos: medium incubated in devices for 5 days with embryos |
Sample Preparation:
Sampleprep ID: | SP001576 |
Sampleprep Summary: | Culture media samples (100 µl) were thawed on ice and prepared using previously described methods. Briefly, 300 µL of dry ice cooled methanol was added to individual culture medium samples and incubated overnight at -80°C; individual samples were spun down to remove proteins and subsequent supernatant used for analyses. Samples were separated and analysed using reverse-phase liquid chromatography connected to a a Thermo Scientific Q Exactive HF (LC-Hybrid Quadrupole-Orbitrap MS/MS) instrument using positive ion mode MS. |
Combined analysis:
Analysis ID | AN002476 | AN002477 |
---|---|---|
Analysis type | MS | MS |
Chromatography type | Reversed phase | Reversed phase |
Chromatography system | Thermo Vanquish | Thermo Vanquish |
Column | Thermo Hypersil Gold (100 x 2.1mm,1.9um) | Thermo Hypersil Gold (100 x 2.1mm,1.9um) |
MS Type | ESI | ESI |
MS instrument type | Orbitrap | Orbitrap |
MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
Ion Mode | POSITIVE | POSITIVE |
Units | peak area | peak area |
Chromatography:
Chromatography ID: | CH001814 |
Instrument Name: | Thermo Vanquish |
Column Name: | Thermo Hypersil Gold (100 x 2.1mm,1.9um) |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS002296 |
Analysis ID: | AN002476 |
Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Full MS analyses were acquired over a mass range of m/z 70-1050 under an ESI positive profile mode. Full mass scan was used at a resolution of 120,000 with a scan rate at ∼3.5 Hz Raw data were imported, processed, normalized, and reviewed using Progenesis QI v.2.1 (Non-linear Dynamics, Newcastle, UK). All FMS sample runs were aligned against a FMS QC pool reference, with alignment to the reference being ≥ 96%, demonstrating the reproducibility of the RPLC column separation method. Peak picking, with a minimum threshold of 100,000 ion intensity, was performed for individual aligned runs based on an aggregate run (representative of all ion peaks detected in all samples). |
Ion Mode: | POSITIVE |
MS ID: | MS002297 |
Analysis ID: | AN002477 |
Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Full MS analyses were acquired over a mass range of m/z 70-1050 under an ESI positive profile mode. Full mass scan was used at a resolution of 120,000 with a scan rate at ∼3.5 Hz Raw data were imported, processed, normalized, and reviewed using Progenesis QI v.2.1 (Non-linear Dynamics, Newcastle, UK). All FMS sample runs were aligned against a FMS QC pool reference, with alignment to the reference being ≥ 96%, demonstrating the reproducibility of the RPLC column separation method. Peak picking, with a minimum threshold of 100,000 ion intensity, was performed for individual aligned runs based on an aggregate run (representative of all ion peaks detected in all samples). |
Ion Mode: | POSITIVE |