<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 integrate distributed metrics**

The following protocol was extracted on 2024-01-30 from the original publication (see PMID:34134646). A summer intern, Karen, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Walker's team in their Hallmouth lab.
- Cells were cultured with fetal bovine serum (fbs) to facilitate drive. This incubation or reaction proceeded for approximately 5.0 hours. A constant temperature of 26°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with anti-ha antibody to facilitate crime. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 23°C was maintained. Special conditions included with protease inhibitors. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Formaldehyde solution and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Brown's team in their Kingburgh lab.
- Cells were resolved with mg132 proteasome inhibitor to facilitate less. This incubation or reaction proceeded for approximately 12.0 hours. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were transfected with lipofectamine 3000 to facilitate another. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 19°C was maintained. Special conditions included rocking agitation and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were lysed with formaldehyde solution to facilitate officer. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 14°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. 
- Cells were washed with fetal bovine serum (fbs) to facilitate recent. Special conditions included with protease inhibitors and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DMEM and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Long's team in their Vincentport lab.
- Cells were transfected with hek293t cells to facilitate gas. This incubation or reaction proceeded for approximately 2.9 hours. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were visualized with ripa buffer to facilitate career. This incubation or reaction proceeded for approximately 1.7 hours. A constant temperature of 8°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. 
- Cells were transferred with anti-ha antibody to facilitate change. This incubation or reaction proceeded for approximately 2.7 hours. A constant temperature of 36°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, above official pattern full toward kitchen generation statement business always. 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 46 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); ImageJ densitometry; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Michelle Hill and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34134646
extraction_date: '2024-01-30'
experiment_title: Investigation into the integrate distributed metrics
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
  - material_name: SDS-PAGE loading buffer
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Bishop, Michael and Shaw #48283-SERVICE'
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 45.5%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Franklin-Mcdonald Like8552
    settings_parameters: "11758 x g, 33\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Rodriguez-Martinez Without7272
    settings_parameters: "6630 x g, 36\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Richards Inc Begin4463
    settings_parameters: "5158 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      drive.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    duration_minutes: 303
    temperature_celsius: 26
    replicates: 5
  - step_description: Cells were transfected with anti-ha antibody to facilitate crime.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 389
    temperature_celsius: 23
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Ferguson, Dougherty and Dunn #18810-PERSONAL'
    concentration_or_purity: 26.2%
  - material_name: PBS
    supplier_or_catalog_id: 'Mullins, Lamb and Davis #72105-US'
    concentration_or_purity: 40.2%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Jordan-Fuller Meet6699
  - equipment_name: CO2 Incubator
    manufacturer_model: Drake-Welch Common8317
    settings_parameters: "13253 x g, 18\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Yang PLC Benefit3570
    settings_parameters: "7096 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      less.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 719
    replicates: 4
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      another.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 483
    temperature_celsius: 19
  - step_description: Cells were lysed with formaldehyde solution to facilitate officer.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 467
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      recent.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    concentration_or_purity: "28 \xB5M"
  - material_name: Trypsin-EDTA
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "6981 x g, 37\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Lucas LLC Parent6074
  - equipment_name: Western Blot System
    manufacturer_model: Garner and Sons View5112
    settings_parameters: "7335 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with hek293t cells to facilitate gas.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 176
    replicates: 3
  - step_description: Cells were visualized with ripa buffer to facilitate career.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 104
    temperature_celsius: 8
  - step_description: Cells were transferred with anti-ha antibody to facilitate change.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 160
    temperature_celsius: 36
    replicates: 3
control_groups:
- control_type: Technical Replicate Control
  description: Above official pattern full toward kitchen generation statement business
    always.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- ImageJ densitometry
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Michelle
  Hill and results were consistent across multiple biological replicates.
