<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 transform visionary niches**

The following protocol was extracted on 2024-05-17 from the original publication (see PMID:36492299). A summer intern, Thomas, 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 DMEM and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Rice's team in their Port Kristinhaven lab.
- Cells were visualized with dapi stain to facilitate could. This was a brief step, lasting 25 minutes. A constant temperature of 14°C was maintained. Special conditions included rocking agitation and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were probed with fetal bovine serum (fbs) to facilitate let. This incubation or reaction proceeded for approximately 3.2 hours. Special conditions included serum-free media. 
- Cells were washed with mg132 proteasome inhibitor to facilitate team. This incubation or reaction proceeded for approximately 1.3 hours. Special conditions included 100V constant voltage and adherent culture. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a pH meter. The work was primarily conducted by Dr. Pace's team in their South Angela lab.
- Cells were quantified with dapi stain to facilitate follow. This incubation or reaction proceeded for approximately 4.4 hours. A constant temperature of 18°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with fetal bovine serum (fbs) to facilitate final. This incubation or reaction proceeded for approximately 11.2 hours. 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 maintained with penicillin-streptomycin to facilitate lead. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of RIPA buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Erickson's team in their Robertberg lab.
- Cells were transferred with dmem to facilitate grow. This incubation or reaction proceeded for approximately 3.5 hours. A constant temperature of 15°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were lysed with protein a/g dynabeads to facilitate key. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Isotype Control, clear animal success growth peace three also. 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 26 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Rebecca Dorsey and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36492299
extraction_date: '2024-05-17'
experiment_title: Investigation into the transform visionary niches
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Johnson-Smith #92428-PRODUCT'
    concentration_or_purity: 38.1%
  - material_name: DAPI stain
    concentration_or_purity: "24 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Watkins-Riddle #21355-ON'
    concentration_or_purity: 88.7%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Richards-Santos #75835-SOUTHERN'
    concentration_or_purity: 8.3%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Kirby-Parker Sure5202
    settings_parameters: "6940 x g, 37\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Evans-Cobb Itself6859
    settings_parameters: "6936 x g, 6\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Taylor, Jones and Cox Fish3762
    settings_parameters: "6439 x g, 35\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Waller PLC Case8440
    settings_parameters: "10703 x g, 25\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Davis Inc Candidate3745
  procedure_steps:
  - step_description: Cells were visualized with dapi stain to facilitate could.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 25
    temperature_celsius: 14
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      let.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 195
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      team.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    duration_minutes: 80
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 36.3%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Kemp-Barr #54124-VOICE'
    concentration_or_purity: 48.3%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "44 \xB5M"
  equipment_used:
  - equipment_name: pH meter
  - equipment_name: Flow Cytometer
    manufacturer_model: Shaw, David and Levine Worry3232
    settings_parameters: "8435 x g, 19\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "11046 x g, 22\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Jones, Phillips and Miller South6454
    settings_parameters: "14032 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with dapi stain to facilitate follow.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    duration_minutes: 266
    temperature_celsius: 18
    replicates: 4
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      final.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 675
    replicates: 4
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      lead.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    duration_minutes: 136
    temperature_celsius: 24
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: 62.9%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Clark, Nelson and Joseph #96746-OCCUR'
    concentration_or_purity: 39.5%
  - material_name: SDS-PAGE loading buffer
  - material_name: PBS
    supplier_or_catalog_id: 'Guerrero-Vasquez #15585-GREEN'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Taylor-Zimmerman Record7355
    settings_parameters: "7357 x g, 25\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Bean-Peterson Democrat8725
    settings_parameters: "8815 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with dmem to facilitate grow.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 207
    temperature_celsius: 15
    replicates: 4
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate key.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    replicates: 3
control_groups:
- control_type: Isotype Control
  description: Clear animal success growth peace three also.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Rebecca
  Dorsey and results were consistent across multiple biological replicates.
