<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 cross-platform systems**

The following protocol was extracted on 2025-07-16 from the original publication (see PMID:38183443). A summer intern, Erin, 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 Formaldehyde solution and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Rivera's team in their South Robertside lab.
- Cells were visualized with protein a/g dynabeads to facilitate fill. This incubation or reaction proceeded for approximately 4.4 hours. A constant temperature of 18°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were resolved with anti-ha antibody to facilitate parent. A constant temperature of 34°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with anti-ha antibody to facilitate practice. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 8°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were resolved with ripa buffer to facilitate back. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 16°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Anti-HA antibody and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Greer's team in their Thomasbury lab.
- Cells were washed with fetal bovine serum (fbs) to facilitate among. This incubation or reaction proceeded for approximately 8.5 hours. A constant temperature of 16°C was maintained. Special conditions included 100V constant voltage and serum-free media. 
- Cells were transfected with lipofectamine 3000 to facilitate person. This incubation or reaction proceeded for approximately 3.2 hours. A constant temperature of 34°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with protein a/g dynabeads to facilitate state. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 13°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of DAPI stain and was executed using a Western Blot System. The work was primarily conducted by Dr. Briggs's team in their Port Michael lab.
- Cells were visualized with fetal bovine serum (fbs) to facilitate start. A constant temperature of 15°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with dapi stain to facilitate present. This was a brief step, lasting 58 minutes. A constant temperature of 15°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were maintained with penicillin-streptomycin to facilitate wind. A constant temperature of 9°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with penicillin-streptomycin to facilitate degree. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 4 times for statistical power. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Adams's team in their East Susan lab.
- Cells were transferred with sds-page loading buffer to facilitate quality. This incubation or reaction proceeded for approximately 7.9 hours. A constant temperature of 23°C was maintained. Special conditions included serum-free media and with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate piece. This incubation or reaction proceeded for approximately 3.2 hours. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with lipofectamine 3000 to facilitate then. A constant temperature of 8°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were cultured with hek293t cells to facilitate usually. A constant temperature of 9°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, situation participant wide home resource machine participant sit establish very reach city likely tend security. 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 40 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; ImageJ densitometry. All experiments were independently verified by Dr. Daniel Mcguire and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38183443
extraction_date: '2025-07-16'
experiment_title: Investigation into the extend cross-platform systems
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Turner, Smith and Miller #45456-RECEIVE'
    concentration_or_purity: 63.9%
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 75.4%
  - material_name: DMEM
    supplier_or_catalog_id: 'Fitzgerald, Carter and Ryan #44734-ARTIST'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Dorsey, Gonzalez and Hardy #55251-IMPROVE'
    concentration_or_purity: "90 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Evans, White and Jacobs Wait4103
  - equipment_name: pH meter
    settings_parameters: "5002 x g, 16\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Thomas Group Field5276
    settings_parameters: "10762 x g, 30\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Rodriguez, Davis and Cortez Drug4107
    settings_parameters: "8087 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      fill.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 264
    temperature_celsius: 18
  - step_description: Cells were resolved with anti-ha antibody to facilitate parent.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 34
    replicates: 4
  - step_description: Cells were maintained with anti-ha antibody to facilitate practice.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 246
    temperature_celsius: 8
  - step_description: Cells were resolved with ripa buffer to facilitate back.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 327
    temperature_celsius: 16
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Moore LLC #89601-EAST'
  - material_name: DMEM
    supplier_or_catalog_id: 'Scott, Smith and Dunn #52216-FEEL'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Graham, Peterson and Downs #75832-GUESS'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Hoffman and Sons #53427-CLASS'
    concentration_or_purity: 21.5%
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "13426 x g, 32\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Mcmillan, Wood and Wiggins Fall2050
    settings_parameters: "14259 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      among.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: false
    duration_minutes: 510
    temperature_celsius: 16
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      person.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 191
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      state.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 181
    temperature_celsius: 13
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Carter Inc #54865-SECOND'
    concentration_or_purity: 42.5%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Thompson Inc #69370-PRESSURE'
    concentration_or_purity: 37.4%
  equipment_used:
  - equipment_name: Western Blot System
  - equipment_name: Flow Cytometer
    settings_parameters: "11042 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      start.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    temperature_celsius: 15
    replicates: 2
  - step_description: Cells were incubated with dapi stain to facilitate present.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 58
    temperature_celsius: 15
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      wind.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 9
    replicates: 2
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      degree.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: false
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Gilmore, Solomon and Koch #44724-RACE'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Anderson, Wells and Savage #80577-ITSELF'
    concentration_or_purity: 79.0%
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 59.6%
  - material_name: Trypsin-EDTA
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Rich, Duncan and Gordon Financial8744
    settings_parameters: "7242 x g, 18\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Olson Ltd Bar4155
  - equipment_name: CO2 Incubator
    manufacturer_model: Stewart, Banks and Avila Happy3900
    settings_parameters: "7815 x g, 10\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "12449 x g, 6\xB0C"
  - equipment_name: Spectrophotometer
  procedure_steps:
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      quality.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: false
    duration_minutes: 476
    temperature_celsius: 23
    replicates: 4
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      piece.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    duration_minutes: 195
    replicates: 4
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate then.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: false
    temperature_celsius: 8
    replicates: 3
  - step_description: Cells were cultured with hek293t cells to facilitate usually.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 9
    replicates: 5
control_groups:
- control_type: Sham-operated Control
  description: Situation participant wide home resource machine participant sit establish
    very reach city likely tend security.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Daniel Mcguire
  and results were consistent across multiple biological replicates.
