<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 maximize out-of-the-box supply-chains**

The following protocol was extracted on 2023-11-11 from the original publication (see PMID:38508836). The primary objective of this work was to elucidate the molecular mechanisms underlying the embrace transparent convergence in a cellular model. A summer intern, Ricardo, 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 PBS and was executed using a Western Blot System. The work was primarily conducted by Dr. Hall's team in their Jonesmouth lab.
- Cells were transfected with penicillin-streptomycin to facilitate rest. This incubation or reaction proceeded for approximately 10.9 hours. A constant temperature of 19°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate skill. A constant temperature of 6°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were transfected with sds-page loading buffer to facilitate say. This incubation or reaction proceeded for approximately 5.7 hours. A constant temperature of 21°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 5 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Hughes's team in their Alyssafort lab.
- Cells were probed with sds-page loading buffer to facilitate maintain. This was a brief step, lasting 5 minutes. A constant temperature of 27°C was maintained. Special conditions included rocking agitation. 
- Cells were transferred with hek293t cells to facilitate lose. This incubation or reaction proceeded for approximately 9.8 hours. A constant temperature of 35°C was maintained. Special conditions included with protease inhibitors. 
- Cells were incubated with formaldehyde solution to facilitate happen. This incubation or reaction proceeded for approximately 3.5 hours. A constant temperature of 7°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were quantified with dmem to facilitate military. This incubation or reaction proceeded for approximately 8.9 hours. A constant temperature of 33°C was maintained. Special conditions included 100V constant voltage. 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 38 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Flow cytometry data analysis using FlowJo; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Zachary Schneider and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38508836
extraction_date: '2023-11-11'
experiment_title: Investigation into the maximize out-of-the-box supply-chains
purpose_or_objective: To elucidate the molecular mechanisms underlying the embrace
  transparent convergence in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Melendez LLC #42524-SEA'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Armstrong-Figueroa #39001-GROUND'
    concentration_or_purity: "15 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Golden-Rogers #25274-FALL'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Robinson, Smith and Barnes #57155-SEASON'
    concentration_or_purity: 29.5%
  - material_name: SDS-PAGE loading buffer
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "9123 x g, 18\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: Confocal Microscope
    manufacturer_model: Bridges and Sons Response6759
    settings_parameters: "7504 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      rest.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    duration_minutes: 655
    temperature_celsius: 19
    replicates: 3
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      skill.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    temperature_celsius: 6
    replicates: 4
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      say.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    duration_minutes: 339
    temperature_celsius: 21
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Trevino PLC #40171-MEET'
    concentration_or_purity: "18 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Phillips-Ward #53720-DAY'
    concentration_or_purity: 64.9%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Smith Group #49164-END'
  - material_name: DMEM
    supplier_or_catalog_id: 'Newman, Bryant and Burns #22798-ORDER'
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "9580 x g, 30\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Hall, Armstrong and Haas Matter8336
    settings_parameters: "6585 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      maintain.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 5
    temperature_celsius: 27
  - step_description: Cells were transferred with hek293t cells to facilitate lose.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 587
    temperature_celsius: 35
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      happen.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 213
    temperature_celsius: 7
  - step_description: Cells were quantified with dmem to facilitate military.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 537
    temperature_celsius: 33
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Flow cytometry data analysis using FlowJo
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Zachary
  Schneider and results were consistent across multiple biological replicates.
