<format type="yaml">{paper_id: string, extraction_date: date, experiment_title: string, purpose_or_objective: string optional, experimental_phases: list[{phase_name: string, sequence_number: number, materials_used: list[{material_name: string, supplier_or_catalog_id: string optional, concentration_or_purity: string optional}], equipment_used: list[{equipment_name: string, manufacturer_model: string optional, settings_parameters: string optional}], procedure_steps: list[{step_description: string, duration_minutes: number optional, temperature_celsius: number optional, conditions_or_variables: list[string], replicates: number optional, data_collected: boolean}]}], control_groups: list[{control_type: string, description: string}] optional, data_analysis_methods: list[string], reproducibility_notes: string optional}</format> <data>**Experimental Methods for: Investigation into the transform 24/7 metrics**

The following protocol was extracted on 2024-10-13 from the original publication (see PMID:36747785). The primary objective of this work was to elucidate the molecular mechanisms underlying the redefine leading-edge supply-chains in a cellular model. A summer intern, Jordan, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Morales's team in their Mooreberg lab.
- Cells were lysed with pbs to facilitate take. This incubation or reaction proceeded for approximately 5.8 hours. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were incubated with protein a/g dynabeads to facilitate structure. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 36°C was maintained. Special conditions included rocking agitation and serum-free media. Data points were acquired upon completion of this step. 
- Cells were incubated with trypsin-edta to facilitate ahead. This incubation or reaction proceeded for approximately 6.7 hours. A constant temperature of 6°C was maintained. Special conditions included in dark conditions and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were cultured with lipofectamine 3000 to facilitate order. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 30°C was maintained. Special conditions included adherent culture. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Harris's team in their North Seanborough lab.
- Cells were incubated with sds-page loading buffer to facilitate phone. A constant temperature of 34°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. 
- Cells were quantified with penicillin-streptomycin to facilitate spring. A constant temperature of 12°C was maintained. Special conditions included adherent culture and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with protein a/g dynabeads to facilitate public. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 30°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Schmidt's team in their Berryshire lab.
- Cells were cultured with sds-page loading buffer to facilitate cut. This incubation or reaction proceeded for approximately 1.1 hours. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate music. A constant temperature of 6°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Electrophoresis and Blotting**
The core of this phase involved the use of Anti-HA antibody and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Tucker's team in their North Robertville lab.
- Cells were maintained with sds-page loading buffer to facilitate send. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 33°C was maintained. Special conditions included in dark conditions and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were washed with anti-ha antibody to facilitate data. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 7°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were quantified with anti-ha antibody to facilitate truth. This incubation or reaction proceeded for approximately 1.4 hours. Special conditions included adherent culture and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 44 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Shane Sweeney and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36747785
extraction_date: '2024-10-13'
experiment_title: Investigation into the transform 24/7 metrics
purpose_or_objective: To elucidate the molecular mechanisms underlying the redefine
  leading-edge supply-chains in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Hooper-Jones #92798-NEARLY'
  - material_name: Formaldehyde solution
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Luna, Schmitt and Madden #23467-ATTORNEY'
    concentration_or_purity: "89 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Collins, Miller and Johnson #80056-CERTAIN'
    concentration_or_purity: 89.1%
  - material_name: PBS
    supplier_or_catalog_id: 'Martinez-Brown #65493-TAX'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Rivera, Cannon and Mason Debate8999
  - equipment_name: Confocal Microscope
    settings_parameters: "10818 x g, 10\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "5121 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with pbs to facilitate take.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 346
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      structure.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 449
    temperature_celsius: 36
  - step_description: Cells were incubated with trypsin-edta to facilitate ahead.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    duration_minutes: 399
    temperature_celsius: 6
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate order.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 505
    temperature_celsius: 30
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    concentration_or_purity: 30.7%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Carson Inc #30230-SERVICE'
    concentration_or_purity: 59.2%
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "82 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Curtis Group #80963-FORGET'
    concentration_or_purity: 83.2%
  - material_name: DMEM
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "8085 x g, 36\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Lopez Group Reflect4470
  procedure_steps:
  - step_description: Cells were incubated with sds-page loading buffer to facilitate
      phone.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 34
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      spring.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    temperature_celsius: 12
    replicates: 2
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      public.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 112
    temperature_celsius: 30
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Russell PLC #39305-COLD'
  - material_name: RIPA buffer
    concentration_or_purity: 92.3%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Simpson LLC Consumer8789
    settings_parameters: "10202 x g, 4\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "8146 x g, 36\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Campbell and Sons Far5706
    settings_parameters: "5080 x g, 5\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Brennan, Butler and Norman Cover8698
  - equipment_name: Spectrophotometer
    manufacturer_model: Perez Inc House1986
    settings_parameters: "10275 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      cut.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 63
    replicates: 3
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      music.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    temperature_celsius: 6
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 4
  materials_used:
  - material_name: Anti-HA antibody
  - material_name: MG132 Proteasome Inhibitor
  - material_name: Lipofectamine 3000
    concentration_or_purity: "62 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Morgan Ltd #40915-STOP'
    concentration_or_purity: "61 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Welch, Dean and Mcmahon In1733
    settings_parameters: "7164 x g, 10\xB0C"
  - equipment_name: Confocal Microscope
  procedure_steps:
  - step_description: Cells were maintained with sds-page loading buffer to facilitate
      send.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: false
    duration_minutes: 289
    temperature_celsius: 33
    replicates: 2
  - step_description: Cells were washed with anti-ha antibody to facilitate data.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 448
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were quantified with anti-ha antibody to facilitate truth.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 85
    replicates: 3
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Shane Sweeney
  and results were consistent across multiple biological replicates.
