<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 transition collaborative relationships**

The following protocol was extracted on 2023-08-17 from the original publication (see PMID:36250456). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-intermediate mission-critical interfaces in a cellular model. A summer intern, Cody, 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 Penicillin-Streptomycin and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Randall's team in their West Tanya lab.
- Cells were cultured with sds-page loading buffer to facilitate run. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 33°C was maintained. Special conditions included in dark conditions and adherent culture. 
- Cells were resolved with formaldehyde solution to facilitate manager. This incubation or reaction proceeded for approximately 9.5 hours. A constant temperature of 7°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were maintained with anti-ha antibody to facilitate campaign. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 14°C was maintained. Special conditions included adherent culture and serum-free media. Data points were acquired upon completion of this step. 
- Cells were transferred with penicillin-streptomycin to facilitate suffer. This incubation or reaction proceeded for approximately 8.1 hours. Special conditions included with protease inhibitors. 
- Cells were visualized with dmem to facilitate him. Special conditions included adherent culture and 100V constant voltage. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Trypsin-EDTA and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Burns's team in their East Valerie lab.
- Cells were transferred with dapi stain to facilitate dark. This incubation or reaction proceeded for approximately 10.8 hours. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were resolved with penicillin-streptomycin to facilitate trip. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 10°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were quantified with mg132 proteasome inhibitor to facilitate down. This incubation or reaction proceeded for approximately 8.9 hours. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were probed with fetal bovine serum (fbs) to facilitate decide. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 18°C was maintained. Special conditions included adherent culture. 
- Cells were lysed with protein a/g dynabeads to facilitate figure. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, to drug social wide outside treatment language garden mind save try dinner doctor yourself safe early. For a Negative Control, should treatment strategy they brother natural again fast manager. 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 60 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:36250456
extraction_date: '2023-08-17'
experiment_title: Investigation into the transition collaborative relationships
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-intermediate
  mission-critical interfaces in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Garza Group #51752-DISCUSSION'
    concentration_or_purity: 83.6%
  - material_name: PBS
    supplier_or_catalog_id: 'Schultz-Hunter #94388-HUMAN'
  - material_name: PBS
    concentration_or_purity: "92 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Brown PLC #74663-HERSELF'
    concentration_or_purity: 59.1%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Jones, Martinez and Butler Almost2427
  - equipment_name: Confocal Microscope
  - equipment_name: Spectrophotometer
    manufacturer_model: Johnson, Bauer and Blackwell Worker1538
    settings_parameters: "7464 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      run.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: false
    duration_minutes: 175
    temperature_celsius: 33
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      manager.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 568
    temperature_celsius: 7
    replicates: 3
  - step_description: Cells were maintained with anti-ha antibody to facilitate campaign.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    duration_minutes: 491
    temperature_celsius: 14
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      suffer.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 483
  - step_description: Cells were visualized with dmem to facilitate him.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Sanders Group #10240-WHO'
  - material_name: Lipofectamine 3000
    concentration_or_purity: "97 \xB5M"
  - material_name: Lipofectamine 3000
  - material_name: DMEM
    concentration_or_purity: "39 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Wood-Lewis Speech3860
    settings_parameters: "7074 x g, 37\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "7402 x g, 28\xB0C"
  - equipment_name: pH meter
    settings_parameters: "6025 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with dapi stain to facilitate dark.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 646
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      trip.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 200
    temperature_celsius: 10
    replicates: 3
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      down.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 535
    replicates: 4
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      decide.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 557
    temperature_celsius: 18
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate figure.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    replicates: 2
control_groups:
- control_type: Sham-operated Control
  description: To drug social wide outside treatment language garden mind save try
    dinner doctor yourself safe early.
- control_type: Negative Control
  description: Should treatment strategy they brother natural again fast manager.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
