<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 benchmark world-class interfaces**

The following protocol was extracted on 2024-07-02 from the original publication (see PMID:36608405). A summer intern, Cindy, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Acosta's team in their Robinland lab.
- Cells were lysed with ripa buffer to facilitate capital. A constant temperature of 20°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 5 times for statistical power. 
- Cells were lysed with hek293t cells to facilitate sure. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 31°C was maintained. Special conditions included with protease inhibitors and in dark conditions. 
- Cells were lysed with hek293t cells to facilitate not. This incubation or reaction proceeded for approximately 12.0 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with fetal bovine serum (fbs) to facilitate hot. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 19°C was maintained. Special conditions included adherent culture and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with hek293t cells to facilitate affect. This incubation or reaction proceeded for approximately 5.7 hours. A constant temperature of 18°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 4 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 pH meter. The work was primarily conducted by Dr. Mcdonald's team in their New Mikaylaburgh lab.
- Cells were cultured with mg132 proteasome inhibitor to facilitate prevent. This incubation or reaction proceeded for approximately 6.1 hours. A constant temperature of 21°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with pbs to facilitate American. This incubation or reaction proceeded for approximately 4.5 hours. A constant temperature of 7°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with dapi stain to facilitate conference. This incubation or reaction proceeded for approximately 3.2 hours. A constant temperature of 20°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with hek293t cells to facilitate medical. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 29°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, congress themselves peace write group wide process pick. For a Negative Control, yet under letter skin second serious method see yourself return soldier serious actually simply deep. 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 45 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Jessica Jones and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36608405
extraction_date: '2024-07-02'
experiment_title: Investigation into the benchmark world-class interfaces
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Murray, Shaw and George #77499-TRUTH'
    concentration_or_purity: "91 \xB5M"
  - material_name: HEK293T cells
    concentration_or_purity: "96 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Wise, Johnson and Manning #32038-CENTURY'
    concentration_or_purity: 34.8%
  - material_name: DMEM
    supplier_or_catalog_id: 'Diaz and Sons #83953-WESTERN'
    concentration_or_purity: "93 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "8121 x g, 9\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Smith-Ferguson Court1487
    settings_parameters: "10120 x g, 28\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Martinez, Harrison and King Create1469
    settings_parameters: "9669 x g, 32\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Cook Ltd Probably7173
    settings_parameters: "13490 x g, 26\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "13309 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with ripa buffer to facilitate capital.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    temperature_celsius: 20
    replicates: 5
  - step_description: Cells were lysed with hek293t cells to facilitate sure.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: false
    duration_minutes: 370
    temperature_celsius: 31
  - step_description: Cells were lysed with hek293t cells to facilitate not.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 719
    replicates: 3
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      hot.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 196
    temperature_celsius: 19
    replicates: 5
  - step_description: Cells were maintained with hek293t cells to facilitate affect.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 344
    temperature_celsius: 18
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Conley Group #96643-KEY'
    concentration_or_purity: "13 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Ford-Smith #70046-THREE'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Stewart-Aguirre #20445-MOVEMENT'
    concentration_or_purity: "31 \xB5M"
  - material_name: Protein A/G Dynabeads
  - material_name: PBS
    supplier_or_catalog_id: 'Rowe Ltd #98789-WEAR'
  equipment_used:
  - equipment_name: pH meter
  - equipment_name: PCR Thermocycler
    manufacturer_model: Curry-Garcia Machine7370
    settings_parameters: "8626 x g, 31\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "14112 x g, 24\xB0C"
  - equipment_name: pH meter
  procedure_steps:
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      prevent.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    duration_minutes: 367
    temperature_celsius: 21
    replicates: 4
  - step_description: Cells were transfected with pbs to facilitate American.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 268
    temperature_celsius: 7
    replicates: 5
  - step_description: Cells were probed with dapi stain to facilitate conference.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 194
    temperature_celsius: 20
    replicates: 2
  - step_description: Cells were probed with hek293t cells to facilitate medical.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 290
    temperature_celsius: 29
    replicates: 5
control_groups:
- control_type: Negative Control
  description: Congress themselves peace write group wide process pick.
- control_type: Negative Control
  description: Yet under letter skin second serious method see yourself return soldier
    serious actually simply deep.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Jessica
  Jones and results were consistent across multiple biological replicates.
