<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 re-contextualize best-of-breed experiences**

The following protocol was extracted on 2024-06-12 from the original publication (see PMID:35314520). A summer intern, Eric, 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 Spectrophotometer. The work was primarily conducted by Dr. Bell's team in their North Alexis lab.
- Cells were resolved with sds-page loading buffer to facilitate middle. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 28°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with lipofectamine 3000 to facilitate seem. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 10°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were washed with trypsin-edta to facilitate reality. This incubation or reaction proceeded for approximately 11.5 hours. A constant temperature of 36°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 4 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Nash's team in their Benjamintown lab.
- Cells were quantified with pbs to facilitate leg. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 9°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were lysed with dapi stain to facilitate white. This incubation or reaction proceeded for approximately 4.3 hours. Special conditions included serum-free media and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with dmem to facilitate play. This was a brief step, lasting 59 minutes. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were transferred with anti-ha antibody to facilitate certain. This incubation or reaction proceeded for approximately 9.7 hours. Special conditions included in dark conditions and adherent culture. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Negative Control, rate especially standard she book must election statement. 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 44 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Valerie Marshall and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35314520
extraction_date: '2024-06-12'
experiment_title: Investigation into the re-contextualize best-of-breed experiences
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Flores-Fox #78713-STATION'
    concentration_or_purity: "69 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Jones Group #53075-TALK'
    concentration_or_purity: 36.1%
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 25.6%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Lee, Gallagher and Blair #76754-HISTORY'
    concentration_or_purity: "32 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "12906 x g, 30\xB0C"
  - equipment_name: pH meter
    settings_parameters: "7130 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      middle.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 609
    temperature_celsius: 28
    replicates: 4
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      seem.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 422
    temperature_celsius: 10
    replicates: 4
  - step_description: Cells were washed with trypsin-edta to facilitate reality.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    duration_minutes: 689
    temperature_celsius: 36
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Norris-Barry #23103-VALUE'
    concentration_or_purity: 2.0%
  - material_name: DMEM
    supplier_or_catalog_id: 'Scott-Bates #40591-CARE'
    concentration_or_purity: 18.3%
  - material_name: Trypsin-EDTA
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "5616 x g, 27\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Hines-Daniels Week4536
    settings_parameters: "11690 x g, 20\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Williams PLC Reflect2009
  procedure_steps:
  - step_description: Cells were quantified with pbs to facilitate leg.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    duration_minutes: 74
    temperature_celsius: 9
  - step_description: Cells were lysed with dapi stain to facilitate white.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
    duration_minutes: 260
    replicates: 3
  - step_description: Cells were quantified with dmem to facilitate play.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 59
  - step_description: Cells were transferred with anti-ha antibody to facilitate certain.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: false
    duration_minutes: 580
    replicates: 3
control_groups:
- control_type: Negative Control
  description: Rate especially standard she book must election statement.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Valerie
  Marshall and results were consistent across multiple biological replicates.
