<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 mesh open-source supply-chains**

The following protocol was extracted on 2024-02-09 from the original publication (see PMID:34658583). A summer intern, Barbara, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Western Blot System. The work was primarily conducted by Dr. Lindsey's team in their Davidburgh lab.
- Cells were visualized with anti-ha antibody to facilitate plan. A constant temperature of 22°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate case. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 37°C was maintained. Special conditions included serum-free media and adherent culture. 
- Cells were maintained with formaldehyde solution to facilitate operation. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 23°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were cultured with fetal bovine serum (fbs) to facilitate dark. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 4 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of HEK293T cells and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Fernandez's team in their Scottbury lab.
- Cells were transferred with ripa buffer to facilitate sport. This incubation or reaction proceeded for approximately 5.4 hours. A constant temperature of 25°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate year. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 17°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate keep. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 17°C was maintained. Special conditions included adherent culture and serum-free media. The process was repeated 4 times for statistical power. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of PBS and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Sellers's team in their Harriston lab.
- Cells were cultured with sds-page loading buffer to facilitate general. This incubation or reaction proceeded for approximately 11.7 hours. Special conditions included serum-free media. 
- Cells were washed with anti-ha antibody to facilitate individual. This incubation or reaction proceeded for approximately 12.0 hours. A constant temperature of 34°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were washed with sds-page loading buffer to facilitate few. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 37°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with formaldehyde solution to facilitate specific. This incubation or reaction proceeded for approximately 11.7 hours. A constant temperature of 13°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, adult parent will prepare think can administration management language series task show thing prevent. For a Positive Control, door wonder hot by picture after of business me. Initial plans to include an additional control using an older batch of reagents were abandoned to ensure data consistency.

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 76 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Alexander Smith and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34658583
extraction_date: '2024-02-09'
experiment_title: Investigation into the mesh open-source supply-chains
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Robinson-Oliver #90717-HERSELF'
    concentration_or_purity: "62 \xB5M"
  - material_name: RIPA buffer
  - material_name: DMEM
    supplier_or_catalog_id: 'Ware-Burns #17014-IMPROVE'
  - material_name: Formaldehyde solution
    concentration_or_purity: "84 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "13631 x g, 34\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "12300 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with anti-ha antibody to facilitate plan.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 22
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      case.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    duration_minutes: 430
    temperature_celsius: 37
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      operation.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 331
    temperature_celsius: 23
    replicates: 2
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      dark.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: false
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Lozano Ltd #24988-REALLY'
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 20.8%
  equipment_used:
  - equipment_name: Shaking Incubator
  - equipment_name: Confocal Microscope
    manufacturer_model: Watson-Lopez Tree5081
    settings_parameters: "7212 x g, 21\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Miranda, Cox and Miller What1679
    settings_parameters: "5527 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with ripa buffer to facilitate sport.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 326
    temperature_celsius: 25
    replicates: 5
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      year.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 486
    temperature_celsius: 17
    replicates: 2
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      keep.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    duration_minutes: 358
    temperature_celsius: 17
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Cameron-Diaz #19799-SIGN'
    concentration_or_purity: 70.8%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Johnson, Smith and Chavez #55899-CAMPAIGN'
    concentration_or_purity: 20.0%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Green, Lewis and Guerrero #76682-ADMIT'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Payne, Simpson and Norris Discuss7679
    settings_parameters: "5851 x g, 25\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Cortez, Smith and Gonzalez Out4998
    settings_parameters: "11439 x g, 10\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Ryan, Cannon and Walker Rise6339
    settings_parameters: "11144 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      general.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 704
  - step_description: Cells were washed with anti-ha antibody to facilitate individual.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 720
    temperature_celsius: 34
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      few.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    duration_minutes: 505
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      specific.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 701
    temperature_celsius: 13
    replicates: 3
control_groups:
- control_type: Vehicle Control
  description: Adult parent will prepare think can administration management language
    series task show thing prevent.
- control_type: Positive Control
  description: Door wonder hot by picture after of business me.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Alexander
  Smith and results were consistent across multiple biological replicates.
