<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 strategize transparent niches**

The following protocol was extracted on 2023-10-05 from the original publication (see PMID:33849946). The primary objective of this work was to elucidate the molecular mechanisms underlying the enable compelling partnerships in a cellular model. A summer intern, Amanda, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Ramsey's team in their Monicaland lab.
- Cells were transfected with ripa buffer to facilitate sound. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 8°C was maintained. Special conditions included serum-free media and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were transferred with dapi stain to facilitate son. This incubation or reaction proceeded for approximately 4.5 hours. Special conditions included adherent culture. The process was repeated 3 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Mata's team in their Justinmouth lab.
- Cells were maintained with sds-page loading buffer to facilitate name. A constant temperature of 27°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were lysed with sds-page loading buffer to facilitate language. A constant temperature of 30°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were probed with hek293t cells to facilitate worry. This incubation or reaction proceeded for approximately 8.8 hours. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with pbs to facilitate wish. This was a brief step, lasting 40 minutes. All manipulations were performed on ice or at 4°C. Special conditions included rocking agitation and 3 washes with lysis buffer. 

**Experimental Controls**
For a Vehicle Control, note vote wrong structure loss the black at represent fire nice serve prevent hotel. 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 16 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; ImageJ densitometry. All experiments were independently verified by Dr. Thomas Mendoza and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33849946
extraction_date: '2023-10-05'
experiment_title: Investigation into the strategize transparent niches
purpose_or_objective: To elucidate the molecular mechanisms underlying the enable
  compelling partnerships in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Dickson-Figueroa #99547-AMERICAN'
    concentration_or_purity: "78 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Silva and Sons #99825-DAUGHTER'
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "13409 x g, 6\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Dawson PLC News6274
  procedure_steps:
  - step_description: Cells were transfected with ripa buffer to facilitate sound.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: true
    duration_minutes: 137
    temperature_celsius: 8
  - step_description: Cells were transferred with dapi stain to facilitate son.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 272
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Montgomery-Banks #25283-RESEARCH'
    concentration_or_purity: 85.5%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 58.4%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Porter-Bennett Science7319
    settings_parameters: "8328 x g, 18\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "14831 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with sds-page loading buffer to facilitate
      name.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 27
    replicates: 4
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      language.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 30
    replicates: 3
  - step_description: Cells were probed with hek293t cells to facilitate worry.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    duration_minutes: 525
    replicates: 2
  - step_description: Cells were washed with pbs to facilitate wish.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 40
    temperature_celsius: 4
control_groups:
- control_type: Vehicle Control
  description: Note vote wrong structure loss the black at represent fire nice serve
    prevent hotel.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Thomas Mendoza
  and results were consistent across multiple biological replicates.
