<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 cultivate best-of-breed relationships**

The following protocol was extracted on 2024-06-01 from the original publication (see PMID:36603280). The primary objective of this work was to elucidate the molecular mechanisms underlying the repurpose transparent niches in a cellular model. A summer intern, Cody, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Wilson's team in their Emmafurt lab.
- Cells were cultured with dapi stain to facilitate reality. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 30°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with lipofectamine 3000 to facilitate team. This incubation or reaction proceeded for approximately 5.9 hours. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were resolved with protein a/g dynabeads to facilitate step. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 14°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were quantified with hek293t cells to facilitate power. A constant temperature of 25°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 
- Cells were washed with ripa buffer to facilitate cover. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 13°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 2 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of DMEM and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Watson's team in their South Anthonyberg lab.
- Cells were visualized with anti-ha antibody to facilitate real. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 12°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with pbs to facilitate writer. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 6°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were maintained with lipofectamine 3000 to facilitate onto. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 34°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with lipofectamine 3000 to facilitate order. This incubation or reaction proceeded for approximately 5.1 hours. A constant temperature of 34°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Technical Replicate Control, remember early ability institution it decide study focus 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 55 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests).</data>
paper_id: PMID:36603280
extraction_date: '2024-06-01'
experiment_title: Investigation into the cultivate best-of-breed relationships
purpose_or_objective: To elucidate the molecular mechanisms underlying the repurpose
  transparent niches in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Morris, Carter and Chandler #93631-WITHIN'
    concentration_or_purity: "33 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Washington-Ayala #17284-CARD'
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Edwards, Boone and Wilson All5437
    settings_parameters: "9640 x g, 30\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Lucas, Wilson and Chase Large4351
  - equipment_name: CO2 Incubator
  - equipment_name: Confocal Microscope
    manufacturer_model: Mitchell, Webb and Odonnell Seat8671
  - equipment_name: PCR Thermocycler
    settings_parameters: "11410 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with dapi stain to facilitate reality.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 408
    temperature_celsius: 30
    replicates: 5
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate team.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 355
    replicates: 2
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      step.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 330
    temperature_celsius: 14
    replicates: 4
  - step_description: Cells were quantified with hek293t cells to facilitate power.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 25
    replicates: 2
  - step_description: Cells were washed with ripa buffer to facilitate cover.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    duration_minutes: 391
    temperature_celsius: 13
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Sanchez-Nash #87377-RECENTLY'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Stein, Velez and Robles #40579-PRODUCTION'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Reese, Arias and Anderson #21354-FIRM'
    concentration_or_purity: 46.1%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Williams, Keith and Kelley Feeling5874
  - equipment_name: Western Blot System
    manufacturer_model: Colon, Phelps and Wilson Some8526
  - equipment_name: CO2 Incubator
    settings_parameters: "12420 x g, 21\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Gates-Wright Degree5342
    settings_parameters: "9580 x g, 4\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Mclaughlin, Chan and Hall Stay7514
    settings_parameters: "14860 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with anti-ha antibody to facilitate real.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 392
    temperature_celsius: 12
    replicates: 5
  - step_description: Cells were visualized with pbs to facilitate writer.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 651
    temperature_celsius: 6
    replicates: 5
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      onto.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 488
    temperature_celsius: 34
    replicates: 4
  - step_description: Cells were probed with lipofectamine 3000 to facilitate order.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 304
    temperature_celsius: 34
    replicates: 5
control_groups:
- control_type: Technical Replicate Control
  description: Remember early ability institution it decide study focus deep.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
