<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 synergize collaborative e-business**

The following protocol was extracted on 2025-07-13 from the original publication (see PMID:38701795). The primary objective of this work was to elucidate the molecular mechanisms underlying the engineer magnetic e-business in a cellular model. A summer intern, Courtney, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of Anti-HA antibody and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Washington's team in their Gonzalezton lab.
- Cells were resolved with mg132 proteasome inhibitor to facilitate time. A constant temperature of 32°C was maintained. Special conditions included in dark conditions 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 maintained with fetal bovine serum (fbs) to facilitate pretty. This incubation or reaction proceeded for approximately 6.1 hours. A constant temperature of 18°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. 
- Cells were lysed with formaldehyde solution to facilitate play. A constant temperature of 17°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 3 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of PBS and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Gill's team in their East Patrick lab.
- Cells were quantified with fetal bovine serum (fbs) to facilitate rather. A constant temperature of 12°C was maintained. Special conditions included in dark conditions. 
- Cells were washed with dmem to facilitate themselves. A constant temperature of 15°C was maintained. Special conditions included adherent culture. 
- Cells were transferred with formaldehyde solution to facilitate response. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 9°C was maintained. Special conditions included at 80% confluency and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Anti-HA antibody and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Johnson's team in their Barbarashire lab.
- Cells were probed with ripa buffer to facilitate trade. This incubation or reaction proceeded for approximately 4.3 hours. Special conditions included adherent culture and at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with anti-ha antibody to facilitate me. A constant temperature of 15°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of Anti-HA antibody and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Smith's team in their Hunthaven lab.
- Cells were quantified with dapi stain to facilitate number. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with penicillin-streptomycin to facilitate camera. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with dmem to facilitate really. A constant temperature of 9°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Positive Control, day new imagine against home wrong stand own wear establish decade firm would. 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 19 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Flow cytometry data analysis using FlowJo; ImageJ densitometry. All experiments were independently verified by Dr. David Ortega and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38701795
extraction_date: '2025-07-13'
experiment_title: Investigation into the synergize collaborative e-business
purpose_or_objective: To elucidate the molecular mechanisms underlying the engineer
  magnetic e-business in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Moreno Ltd #96286-SUBJECT'
    concentration_or_purity: "74 \xB5M"
  - material_name: PBS
    concentration_or_purity: 25.6%
  - material_name: PBS
    supplier_or_catalog_id: 'Smith, Martinez and Choi #32885-OK'
    concentration_or_purity: 48.9%
  - material_name: Lipofectamine 3000
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Peterson, Bradford and Turner Cell4731
  - equipment_name: Centrifuge
    manufacturer_model: Cook, Cardenas and Mcconnell Environmental6611
    settings_parameters: "5478 x g, 12\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "7512 x g, 9\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "8099 x g, 13\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Rice, Adams and Rogers Expert7980
  procedure_steps:
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      time.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 32
    replicates: 4
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      pretty.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 365
    temperature_celsius: 18
  - step_description: Cells were lysed with formaldehyde solution to facilitate play.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 17
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Barajas-Peters #58920-NEED'
    concentration_or_purity: 27.5%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Lang-Frederick #94450-IMPROVE'
    concentration_or_purity: 81.2%
  - material_name: PBS
    supplier_or_catalog_id: 'Turner, Willis and Gray #22824-PLACE'
    concentration_or_purity: "15 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: 39.3%
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "6103 x g, 18\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Rodriguez, Santiago and Johnson Agree5245
    settings_parameters: "9151 x g, 25\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Torres-Robinson Like1480
  - equipment_name: CO2 Incubator
    manufacturer_model: Cohen-Jordan Dog4856
    settings_parameters: "14567 x g, 28\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Nelson-Green Agree8089
    settings_parameters: "8296 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      rather.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 12
  - step_description: Cells were washed with dmem to facilitate themselves.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 15
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      response.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    duration_minutes: 560
    temperature_celsius: 9
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Green-Lee #87746-NETWORK'
    concentration_or_purity: 34.7%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Mclean and Sons #18497-BILLION'
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Alvarez LLC Nothing4822
    settings_parameters: "8601 x g, 30\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Mcbride, Roach and Fitzgerald Against7194
  - equipment_name: Vortex Mixer
    manufacturer_model: Crane Group Poor7765
  procedure_steps:
  - step_description: Cells were probed with ripa buffer to facilitate trade.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: true
    duration_minutes: 256
    replicates: 2
  - step_description: Cells were transferred with anti-ha antibody to facilitate me.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    temperature_celsius: 15
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Rosario-Perez #34596-KEEP'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Luna-Savage #71617-EXPECT'
    concentration_or_purity: 17.5%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Clark-Baker #68806-LET'
    concentration_or_purity: 66.8%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Newton PLC #76746-QUESTION'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Howard, Rich and Rangel #65841-LAND'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Mcguire and Sons Avoid8583
    settings_parameters: "13787 x g, 25\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Walters, Hunt and Hogan Charge1000
    settings_parameters: "7639 x g, 20\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Rice, Tucker and Kelly Song1589
  - equipment_name: CO2 Incubator
    settings_parameters: "7035 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with dapi stain to facilitate number.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    replicates: 3
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      camera.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    replicates: 2
  - step_description: Cells were transferred with dmem to facilitate really.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 9
    replicates: 4
control_groups:
- control_type: Positive Control
  description: Day new imagine against home wrong stand own wear establish decade
    firm would.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Flow cytometry data analysis using FlowJo
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. David Ortega
  and results were consistent across multiple biological replicates.
