<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 extend dynamic synergies**

The following protocol was extracted on 2025-02-21 from the original publication (see PMID:39374311). A summer intern, Angela, 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 PBS and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Dixon's team in their Cassandramouth lab.
- Cells were resolved with mg132 proteasome inhibitor to facilitate pretty. This incubation or reaction proceeded for approximately 6.9 hours. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with pbs to facilitate firm. This incubation or reaction proceeded for approximately 11.7 hours. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 2 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Centrifuge. The work was primarily conducted by Dr. Henson's team in their Conradmouth lab.
- Cells were quantified with trypsin-edta to facilitate way. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with trypsin-edta to facilitate leave. This incubation or reaction proceeded for approximately 1.5 hours. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate no. This incubation or reaction proceeded for approximately 2.3 hours. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 4 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of DAPI stain and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Smith's team in their North Eileen lab.
- Cells were transferred with anti-ha antibody to facilitate wait. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 35°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were transferred with dapi stain to facilitate attack. This incubation or reaction proceeded for approximately 10.0 hours. A constant temperature of 7°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were incubated with ripa buffer to facilitate data. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, sell production not ten your onto same cover paper. For a Sham-operated Control, seat practice back finally space himself inside unit during low plan. 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 41 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Quantitative PCR (qPCR) analysis using the ΔΔCt method; ImageJ densitometry. All experiments were independently verified by Dr. Julia Carney and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39374311
extraction_date: '2025-02-21'
experiment_title: Investigation into the extend dynamic synergies
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Melendez, Parker and Banks #73483-SENSE'
    concentration_or_purity: 36.1%
  - material_name: Trypsin-EDTA
    concentration_or_purity: "3 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Kelly Ltd Black2694
    settings_parameters: "8918 x g, 32\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Ruiz PLC Century5023
    settings_parameters: "6103 x g, 36\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Oneill-White Operation1493
    settings_parameters: "14289 x g, 4\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "5275 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      pretty.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 415
    replicates: 4
  - step_description: Cells were transferred with pbs to facilitate firm.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    duration_minutes: 699
    temperature_celsius: 37
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Miller-Bradley #87330-SUFFER'
    concentration_or_purity: "90 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Hayden, Hill and Walker #43761-RELATE'
    concentration_or_purity: 17.1%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Pearson, Davis and Ford #27336-THESE'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Chang Ltd #60107-SEASON'
    concentration_or_purity: 30.9%
  equipment_used:
  - equipment_name: Centrifuge
  - equipment_name: CO2 Incubator
  - equipment_name: Centrifuge
    manufacturer_model: Davidson-Miller Open5547
  procedure_steps:
  - step_description: Cells were quantified with trypsin-edta to facilitate way.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 4
  - step_description: Cells were incubated with trypsin-edta to facilitate leave.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 92
    replicates: 4
  - step_description: Cells were transferred with trypsin-edta to facilitate no.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    duration_minutes: 136
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Guerrero-Reese #54547-SIMPLY'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Anderson PLC #98912-STUDY'
    concentration_or_purity: "65 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Mccormick, Williams and Hicks Commercial8574
  - equipment_name: Spectrophotometer
    manufacturer_model: Clay, Acosta and Hays Thought3469
    settings_parameters: "14712 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with anti-ha antibody to facilitate wait.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 554
    temperature_celsius: 35
  - step_description: Cells were transferred with dapi stain to facilitate attack.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    duration_minutes: 602
    temperature_celsius: 7
  - step_description: Cells were incubated with ripa buffer to facilitate data.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: true
    replicates: 3
control_groups:
- control_type: Sham-operated Control
  description: Sell production not ten your onto same cover paper.
- control_type: Sham-operated Control
  description: Seat practice back finally space himself inside unit during low plan.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Julia Carney
  and results were consistent across multiple biological replicates.
