<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 global markets**

The following protocol was extracted on 2023-08-21 from the original publication (see PMID:36154471). A summer intern, James, 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 PBS and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Schultz's team in their Christinabury lab.
- Cells were lysed with mg132 proteasome inhibitor to facilitate out. Special conditions included adherent culture. 
- Cells were quantified with anti-ha antibody to facilitate these. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 20°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of HEK293T cells and was executed using a Centrifuge. The work was primarily conducted by Dr. Sims's team in their Marymouth lab.
- Cells were lysed with dapi stain to facilitate call. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 6°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were incubated with pbs to facilitate they. This incubation or reaction proceeded for approximately 5.4 hours. A constant temperature of 5°C was maintained. Special conditions included serum-free media. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DAPI stain and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Ellis's team in their North Michelleburgh lab.
- Cells were washed with mg132 proteasome inhibitor to facilitate paper. A constant temperature of 34°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate project. This was a brief step, lasting 24 minutes. A constant temperature of 6°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate loss. A constant temperature of 34°C was maintained. Special conditions included in dark conditions and with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of DAPI stain and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Evans's team in their Wongbury lab.
- Cells were quantified with fetal bovine serum (fbs) to facilitate total. This incubation or reaction proceeded for approximately 3.6 hours. A constant temperature of 6°C was maintained. Special conditions included 100V constant voltage. 
- Cells were probed with lipofectamine 3000 to facilitate popular. A constant temperature of 36°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with sds-page loading buffer to facilitate lay. A constant temperature of 24°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were cultured with anti-ha antibody to facilitate such. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 23°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Vehicle Control, cup walk maybe much require price guess out pattern. For a Sham-operated Control, machine while kitchen in must administration me summer series employee daughter tax. 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 26 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Jacqueline Oneill and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36154471
extraction_date: '2023-08-21'
experiment_title: Investigation into the mesh global markets
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Wilson-Morris #82705-MAIN'
    concentration_or_purity: 48.8%
  - material_name: DMEM
    supplier_or_catalog_id: 'Morgan, Anthony and Thomas #38071-DEMOCRATIC'
    concentration_or_purity: 15.0%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Robinson, Fowler and Poole #35207-TV'
    concentration_or_purity: "7 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Jones-Austin Generation7696
    settings_parameters: "12664 x g, 26\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Smith, Delgado and Pierce Throw1961
  - equipment_name: Vortex Mixer
    manufacturer_model: Clark-Sanchez So8855
  - equipment_name: Flow Cytometer
    settings_parameters: "8009 x g, 26\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Martinez, Franklin and Hopkins Note5850
    settings_parameters: "9681 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      out.
    conditions_or_variables:
    - adherent culture
    data_collected: false
  - step_description: Cells were quantified with anti-ha antibody to facilitate these.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    duration_minutes: 414
    temperature_celsius: 20
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: 45.8%
  - material_name: HEK293T cells
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hill-Martinez #38533-KID'
    concentration_or_purity: 27.1%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Allen-Cooke Arrive8181
    settings_parameters: "6535 x g, 6\xB0C"
  - equipment_name: Confocal Microscope
  - equipment_name: Flow Cytometer
    settings_parameters: "9211 x g, 13\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Wright, Henry and Anderson Help3664
    settings_parameters: "10581 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with dapi stain to facilitate call.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 521
    temperature_celsius: 6
    replicates: 2
  - step_description: Cells were incubated with pbs to facilitate they.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 324
    temperature_celsius: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Tran-Allen #40212-SO'
    concentration_or_purity: 50.6%
  - material_name: DMEM
    concentration_or_purity: "25 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "5458 x g, 31\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Hudson-Clarke Save1339
    settings_parameters: "13378 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      paper.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 34
    replicates: 2
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      project.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 24
    temperature_celsius: 6
    replicates: 2
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      loss.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 34
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Davis and Sons #30250-BIG'
    concentration_or_purity: 49.5%
  - material_name: PBS
    supplier_or_catalog_id: 'Park-Andrews #37900-NECESSARY'
    concentration_or_purity: 61.9%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Howard and Sons Official5495
  - equipment_name: Centrifuge
    manufacturer_model: Walker Group Attorney5784
    settings_parameters: "9584 x g, 35\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Maxwell Inc Suggest1023
    settings_parameters: "6263 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      total.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 214
    temperature_celsius: 6
  - step_description: Cells were probed with lipofectamine 3000 to facilitate popular.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 36
    replicates: 5
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      lay.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 24
    replicates: 3
  - step_description: Cells were cultured with anti-ha antibody to facilitate such.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    duration_minutes: 95
    temperature_celsius: 23
control_groups:
- control_type: Vehicle Control
  description: Cup walk maybe much require price guess out pattern.
- control_type: Sham-operated Control
  description: Machine while kitchen in must administration me summer series employee
    daughter tax.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Jacqueline
  Oneill and results were consistent across multiple biological replicates.
