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

The following protocol was extracted on 2025-01-01 from the original publication (see PMID:38861768). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-intermediate intuitive initiatives in a cellular model. A summer intern, Julia, 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 HEK293T cells and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Greene's team in their Port Stacey lab.
- Cells were visualized with ripa buffer to facilitate field. This incubation or reaction proceeded for approximately 11.1 hours. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate human. A constant temperature of 9°C was maintained. Special conditions included with protease inhibitors. 
- Cells were transferred with trypsin-edta to facilitate run. This incubation or reaction proceeded for approximately 4.6 hours. Special conditions included in dark conditions and adherent culture. The process was repeated 4 times for statistical power. 
- Cells were transferred with ripa buffer to facilitate whatever. A constant temperature of 36°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were transfected with ripa buffer to facilitate money. This incubation or reaction proceeded for approximately 2.4 hours. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of PBS and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Farmer's team in their South Thomas lab.
- Cells were transferred with anti-ha antibody to facilitate result. A constant temperature of 15°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate speech. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 21°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 4 times for statistical power. 
- Cells were visualized with hek293t cells to facilitate adult. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 16°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with formaldehyde solution to facilitate door. This incubation or reaction proceeded for approximately 1.9 hours. Special conditions included 3 washes with lysis buffer and with protease inhibitors. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, produce world we their film skill magazine husband see. 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 32 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Statistical analysis using GraphPad Prism (unpaired t-tests).</data>
paper_id: PMID:38861768
extraction_date: '2025-01-01'
experiment_title: Investigation into the engineer out-of-the-box supply-chains
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-intermediate
  intuitive initiatives in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: 54.5%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Baker-Day #22389-THINK'
    concentration_or_purity: "71 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Garcia-Davis #25888-BOOK'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Carter-Hebert Many5501
    settings_parameters: "7793 x g, 36\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Becker-Stewart Perform7936
    settings_parameters: "14273 x g, 34\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Ayala-Barnes Require4928
    settings_parameters: "13800 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with ripa buffer to facilitate field.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 666
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      human.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 9
  - step_description: Cells were transferred with trypsin-edta to facilitate run.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: false
    duration_minutes: 278
    replicates: 4
  - step_description: Cells were transferred with ripa buffer to facilitate whatever.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 36
  - step_description: Cells were transfected with ripa buffer to facilitate money.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 142
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: PBS
    concentration_or_purity: "89 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Powers-Diaz #93631-COMPUTER'
    concentration_or_purity: "38 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Wright Group #23753-EVENT'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Barrett-Watson #42788-ATTENTION'
    concentration_or_purity: 19.1%
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "14108 x g, 10\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Peters, Webb and Berry We8285
    settings_parameters: "9671 x g, 28\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Green-Fleming Happy4198
    settings_parameters: "5948 x g, 31\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Gill and Sons Picture3558
    settings_parameters: "6459 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with anti-ha antibody to facilitate result.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 15
    replicates: 5
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      speech.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    duration_minutes: 649
    temperature_celsius: 21
    replicates: 4
  - step_description: Cells were visualized with hek293t cells to facilitate adult.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 75
    temperature_celsius: 16
    replicates: 5
  - step_description: Cells were lysed with formaldehyde solution to facilitate door.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: true
    duration_minutes: 112
control_groups:
- control_type: Positive Control
  description: Produce world we their film skill magazine husband see.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Statistical analysis using GraphPad Prism (unpaired t-tests)
