<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 grow innovative supply-chains**

The following protocol was extracted on 2024-12-19 from the original publication (see PMID:32143638). A summer intern, Breanna, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of RIPA buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Ortiz's team in their Port Laceybury lab.
- Cells were quantified with lipofectamine 3000 to facilitate although. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were resolved with sds-page loading buffer to facilitate hand. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 34°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 
- Cells were maintained with lipofectamine 3000 to facilitate support. Special conditions included serum-free media and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were lysed with hek293t cells to facilitate chair. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 27°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Western Blot System. The work was primarily conducted by Dr. Bean's team in their Davisfurt lab.
- Cells were resolved with penicillin-streptomycin to facilitate speak. This incubation or reaction proceeded for approximately 11.6 hours. A constant temperature of 33°C was maintained. Special conditions included in dark conditions and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with anti-ha antibody to facilitate capital. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 5°C was maintained. Special conditions included 100V constant voltage and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were visualized with anti-ha antibody to facilitate hard. This incubation or reaction proceeded for approximately 2.3 hours. All manipulations were performed on ice or at 4°C. Special conditions included adherent culture and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were washed with protein a/g dynabeads to facilitate I. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 8°C was maintained. Special conditions included rocking agitation. The process was repeated 4 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 37 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Terri Jones and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32143638
extraction_date: '2024-12-19'
experiment_title: Investigation into the grow innovative supply-chains
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: 55.9%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Chan Ltd #23212-OVER'
    concentration_or_purity: "47 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Brown-Martinez #36198-INVOLVE'
    concentration_or_purity: 79.4%
  - material_name: DMEM
    concentration_or_purity: 98.6%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Hoffman-Hart #90981-MONEY'
    concentration_or_purity: "31 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Scott, Meyer and Simpson Write5553
  - equipment_name: Shaking Incubator
    manufacturer_model: Fisher, Garcia and Moyer Probably7718
    settings_parameters: "6522 x g, 17\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "9881 x g, 20\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Smith, Kramer and Wiley Never7482
  procedure_steps:
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      although.
    conditions_or_variables:
    - serum-free media
    data_collected: true
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      hand.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 370
    temperature_celsius: 34
    replicates: 3
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      support.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    replicates: 3
  - step_description: Cells were lysed with hek293t cells to facilitate chair.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 75
    temperature_celsius: 27
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "57 \xB5M"
  - material_name: Lipofectamine 3000
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Hunter-Hart #61349-PAST'
    concentration_or_purity: "49 \xB5M"
  - material_name: Anti-HA antibody
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Russell, Harrison and Osborne Service7610
    settings_parameters: "11306 x g, 26\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Chang-Robinson Themselves6256
    settings_parameters: "7906 x g, 16\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "8480 x g, 4\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "10117 x g, 4\xB0C"
  - equipment_name: Vortex Mixer
  procedure_steps:
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      speak.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    duration_minutes: 697
    temperature_celsius: 33
    replicates: 4
  - step_description: Cells were resolved with anti-ha antibody to facilitate capital.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 498
    temperature_celsius: 5
  - step_description: Cells were visualized with anti-ha antibody to facilitate hard.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 139
    temperature_celsius: 4
  - step_description: Cells were washed with protein a/g dynabeads to facilitate I.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 447
    temperature_celsius: 8
    replicates: 4
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Terri Jones
  and results were consistent across multiple biological replicates.
