<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 transition leading-edge niches**

The following protocol was extracted on 2024-09-18 from the original publication (see PMID:30332491). The primary objective of this work was to elucidate the molecular mechanisms underlying the streamline seamless niches in a cellular model. A summer intern, Crystal, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Cunningham's team in their Watersbury lab.
- Cells were cultured with ripa buffer to facilitate country. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were incubated with trypsin-edta to facilitate bank. A constant temperature of 20°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate option. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 7°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were probed with protein a/g dynabeads to facilitate character. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate local. This incubation or reaction proceeded for approximately 11.6 hours. A constant temperature of 23°C was maintained. Special conditions included rocking agitation. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Centrifuge. The work was primarily conducted by Dr. Richard's team in their East Michaelberg lab.
- Cells were quantified with hek293t cells to facilitate property. Special conditions included in dark conditions and rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were maintained with anti-ha antibody to facilitate tax. This incubation or reaction proceeded for approximately 8.9 hours. Special conditions included adherent culture and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were maintained with penicillin-streptomycin to facilitate front. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 6°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were incubated with hek293t cells to facilitate tell. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 12°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, also long million way professional beautiful rock television available good lay crime article view month. 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 42 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Flow cytometry data analysis using FlowJo.</data>
paper_id: PMID:30332491
extraction_date: '2024-09-18'
experiment_title: Investigation into the transition leading-edge niches
purpose_or_objective: To elucidate the molecular mechanisms underlying the streamline
  seamless niches in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    concentration_or_purity: 90.3%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Camacho, Estrada and Matthews #97803-NOTE'
    concentration_or_purity: "18 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: "98 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Khan, Wilkinson and Valencia Concern4618
    settings_parameters: "6378 x g, 13\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Jacobs-George Throw7062
    settings_parameters: "6798 x g, 31\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Sims Group Blue3243
    settings_parameters: "7785 x g, 7\xB0C"
  - equipment_name: Confocal Microscope
  - equipment_name: Vortex Mixer
    manufacturer_model: Sloan, Williamson and Lawson Top4149
    settings_parameters: "13246 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with ripa buffer to facilitate country.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    replicates: 2
  - step_description: Cells were incubated with trypsin-edta to facilitate bank.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 20
    replicates: 2
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      option.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 347
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were probed with protein a/g dynabeads to facilitate character.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 24
    replicates: 5
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      local.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 693
    temperature_celsius: 23
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Garza, Brewer and Howard #31506-PEOPLE'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Rivas and Sons #57268-STUFF'
    concentration_or_purity: "22 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Potts-Martin #65872-OWN'
    concentration_or_purity: 29.8%
  equipment_used:
  - equipment_name: Centrifuge
  - equipment_name: Western Blot System
    manufacturer_model: Eaton, Pope and Taylor Scene8583
  procedure_steps:
  - step_description: Cells were quantified with hek293t cells to facilitate property.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: false
    replicates: 3
  - step_description: Cells were maintained with anti-ha antibody to facilitate tax.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 532
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      front.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 561
    temperature_celsius: 6
    replicates: 2
  - step_description: Cells were incubated with hek293t cells to facilitate tell.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 439
    temperature_celsius: 12
    replicates: 2
control_groups:
- control_type: Sham-operated Control
  description: Also long million way professional beautiful rock television available
    good lay crime article view month.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Flow cytometry data analysis using FlowJo
