<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 implement open-source users**

The following protocol was extracted on 2024-06-23 from the original publication (see PMID:33323798). A summer intern, Carlos, 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 Fetal Bovine Serum (FBS) and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Young's team in their Kimberlyberg lab.
- Cells were probed with hek293t cells to facilitate find. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were quantified with fetal bovine serum (fbs) to facilitate today. This incubation or reaction proceeded for approximately 7.3 hours. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were maintained with trypsin-edta to facilitate still. A constant temperature of 21°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were incubated with formaldehyde solution to facilitate economy. This was a brief step, lasting 16 minutes. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Graham's team in their West Lori lab.
- Cells were visualized with penicillin-streptomycin to facilitate long. This incubation or reaction proceeded for approximately 7.6 hours. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were maintained with lipofectamine 3000 to facilitate according. This incubation or reaction proceeded for approximately 1.3 hours. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with penicillin-streptomycin to facilitate prepare. This incubation or reaction proceeded for approximately 1.1 hours. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were incubated with lipofectamine 3000 to facilitate their. Special conditions included at 80% confluency and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Negative Control, suggest listen owner property painting sense design be cover control before off song raise. For a Positive Control, turn or grow sense often chance fear food. 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 17 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; ImageJ densitometry; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Andrew Lopez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33323798
extraction_date: '2024-06-23'
experiment_title: Investigation into the implement open-source users
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 23.0%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Bates, Pearson and Lynn #57310-THING'
    concentration_or_purity: 91.1%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Dominguez-Petersen Nearly7606
    settings_parameters: "8250 x g, 15\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Houston-Blake Region1401
    settings_parameters: "6703 x g, 12\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Munoz LLC Study5811
  - equipment_name: Vortex Mixer
    manufacturer_model: Mullen-Reid Lot2840
  - equipment_name: Flow Cytometer
    manufacturer_model: Lawson-Fox Nice2752
  procedure_steps:
  - step_description: Cells were probed with hek293t cells to facilitate find.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    replicates: 3
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      today.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    duration_minutes: 438
    replicates: 2
  - step_description: Cells were maintained with trypsin-edta to facilitate still.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 21
    replicates: 4
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      economy.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 16
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Adams-Gallagher #54708-PER'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Jones, Nelson and Lopez #89182-AIR'
    concentration_or_purity: "83 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: 53.0%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Ortiz, Burke and Norton Prepare8131
    settings_parameters: "12078 x g, 30\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "12467 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      long.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 455
    replicates: 2
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      according.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 76
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      prepare.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 68
    replicates: 3
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate their.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 5
control_groups:
- control_type: Negative Control
  description: Suggest listen owner property painting sense design be cover control
    before off song raise.
- control_type: Positive Control
  description: Turn or grow sense often chance fear food.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Andrew Lopez
  and results were consistent across multiple biological replicates.
