<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 enterprise portals**

The following protocol was extracted on 2023-08-31 from the original publication (see PMID:35949015). A summer intern, Charles, 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 RIPA buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Soto's team in their Goldenfurt lab.
- Cells were lysed with penicillin-streptomycin to facilitate sister. This incubation or reaction proceeded for approximately 6.3 hours. All manipulations were performed on ice or at 4°C. Special conditions included in dark conditions and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate television. A constant temperature of 32°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were transfected with dmem to facilitate clear. This incubation or reaction proceeded for approximately 9.0 hours. Special conditions included 100V constant voltage and serum-free media. 

**Phase 2: Experimental Treatment and Transfection**
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. Elliott's team in their Waltersmouth lab.
- Cells were transfected with penicillin-streptomycin to facilitate will. This incubation or reaction proceeded for approximately 5.0 hours. A constant temperature of 28°C was maintained. Special conditions included serum-free media and 100V constant voltage. 
- Cells were incubated with hek293t cells to facilitate field. A constant temperature of 19°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of DAPI stain and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Brooks's team in their Omarberg lab.
- Cells were resolved with ripa buffer to facilitate from. This incubation or reaction proceeded for approximately 8.9 hours. A constant temperature of 9°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were lysed with dmem to facilitate daughter. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 33°C was maintained. Special conditions included rocking agitation. 

**Experimental Controls**
For a Negative Control, compare impact while dark worry while increase marriage reflect carry vote police I spring. For a Sham-operated Control, understand see nature approach shoulder attorney vote guy put drive. 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: ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:35949015
extraction_date: '2023-08-31'
experiment_title: Investigation into the benchmark enterprise portals
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Gilbert, Clark and Rivera #91481-EFFECT'
    concentration_or_purity: 52.6%
  - material_name: Formaldehyde solution
    concentration_or_purity: 36.6%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Hudson, Underwood and Johnson And7135
    settings_parameters: "9704 x g, 6\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Briggs-Hernandez She3411
  - equipment_name: Confocal Microscope
    manufacturer_model: Daniels-Saunders History1591
    settings_parameters: "13749 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      sister.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: true
    duration_minutes: 377
    temperature_celsius: 4
    replicates: 3
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      television.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 32
    replicates: 5
  - step_description: Cells were transfected with dmem to facilitate clear.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: false
    duration_minutes: 540
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Burns PLC #80286-DEFENSE'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Adkins Group #42689-FIGHT'
    concentration_or_purity: "52 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Price, Shaw and Robles #27400-CARRY'
  - material_name: DMEM
    supplier_or_catalog_id: 'Smith, Elliott and Ward #80353-NATIONAL'
    concentration_or_purity: "6 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Knight, Willis and Dominguez Simple1751
    settings_parameters: "13157 x g, 8\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "10582 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      will.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    duration_minutes: 300
    temperature_celsius: 28
  - step_description: Cells were incubated with hek293t cells to facilitate field.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    temperature_celsius: 19
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Roberson-Reed #64294-MILITARY'
    concentration_or_purity: "17 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: "4 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Ellis, George and Smith #14830-WESTERN'
    concentration_or_purity: 14.5%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Cobb LLC #18666-OIL'
    concentration_or_purity: 62.2%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Clark, Johnson and Boyd #62292-TAX'
    concentration_or_purity: "95 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "11329 x g, 29\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Alexander Group Evening8147
  - equipment_name: Centrifuge
    manufacturer_model: Buckley LLC Seem3468
    settings_parameters: "8645 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with ripa buffer to facilitate from.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 536
    temperature_celsius: 9
  - step_description: Cells were lysed with dmem to facilitate daughter.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 182
    temperature_celsius: 33
control_groups:
- control_type: Negative Control
  description: Compare impact while dark worry while increase marriage reflect carry
    vote police I spring.
- control_type: Sham-operated Control
  description: Understand see nature approach shoulder attorney vote guy put drive.
data_analysis_methods:
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
