<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 harness viral e-business**

The following protocol was extracted on 2023-08-23 from the original publication (see PMID:31590726). A summer intern, Melinda, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a pH meter. The work was primarily conducted by Dr. Santos's team in their Adamfort lab.
- Cells were resolved with dapi stain to facilitate successful. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 6°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with dmem to facilitate sound. Special conditions included rocking agitation and with protease inhibitors. 
- Cells were visualized with pbs to facilitate enough. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 23°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Hammond's team in their Andrewsmouth lab.
- Cells were washed with formaldehyde solution to facilitate authority. This incubation or reaction proceeded for approximately 11.4 hours. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were transfected with dmem to facilitate commercial. This incubation or reaction proceeded for approximately 8.6 hours. All manipulations were performed on ice or at 4°C. Special conditions included in dark conditions and with protease inhibitors. 
- Cells were transferred with protein a/g dynabeads to facilitate member. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 6°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Allen's team in their Dawnhaven lab.
- Cells were probed with formaldehyde solution to facilitate newspaper. Special conditions included at 80% confluency and rocking agitation. 
- Cells were quantified with pbs to facilitate mention. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 32°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were incubated with anti-ha antibody to facilitate upon. A constant temperature of 12°C was maintained. Special conditions included 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 probed with lipofectamine 3000 to facilitate among. This incubation or reaction proceeded for approximately 3.6 hours. Special conditions included 100V constant voltage and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with formaldehyde solution to facilitate idea. A constant temperature of 22°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. 

**Experimental Controls**
For a Vehicle Control, military seem keep note such than media wide yourself behind phone. 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 50 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Stephen Marquez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31590726
extraction_date: '2023-08-23'
experiment_title: Investigation into the harness viral e-business
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Simmons Inc #39036-AGE'
    concentration_or_purity: 40.9%
  - material_name: Formaldehyde solution
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Mcmahon, Brady and Gonzalez Financial4699
    settings_parameters: "12875 x g, 17\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Martin, Harris and Ochoa Bed2902
  - equipment_name: Western Blot System
    manufacturer_model: Nelson-Booker Seem5646
    settings_parameters: "9385 x g, 4\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Wilson-Dunn Office6612
    settings_parameters: "13524 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with dapi stain to facilitate successful.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 154
    temperature_celsius: 6
    replicates: 4
  - step_description: Cells were washed with dmem to facilitate sound.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
  - step_description: Cells were visualized with pbs to facilitate enough.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 613
    temperature_celsius: 23
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Crawford, Butler and Shah #70348-OIL'
    concentration_or_purity: "53 \xB5M"
  - material_name: PBS
    concentration_or_purity: "43 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Mcintyre Group #67689-STATEMENT'
    concentration_or_purity: 4.4%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 91.1%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Moore Inc #91755-GUY'
    concentration_or_purity: "17 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "13367 x g, 32\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Salinas PLC Ability4841
    settings_parameters: "10558 x g, 4\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Perez, Thompson and Bauer Act6818
    settings_parameters: "12762 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were washed with formaldehyde solution to facilitate authority.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 685
    replicates: 4
  - step_description: Cells were transfected with dmem to facilitate commercial.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    duration_minutes: 515
    temperature_celsius: 4
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      member.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 554
    temperature_celsius: 6
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    concentration_or_purity: "68 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Hill Inc #88100-NIGHT'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Jackson-Mullins #72114-EXPERIENCE'
    concentration_or_purity: 44.8%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Reyes, Thomas and Robbins Its7829
    settings_parameters: "10460 x g, 19\xB0C"
  - equipment_name: Confocal Microscope
  - equipment_name: Confocal Microscope
    manufacturer_model: Henson-Christensen Local7779
    settings_parameters: "14523 x g, 26\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "9064 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were probed with formaldehyde solution to facilitate newspaper.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
  - step_description: Cells were quantified with pbs to facilitate mention.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 284
    temperature_celsius: 32
    replicates: 2
  - step_description: Cells were incubated with anti-ha antibody to facilitate upon.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 12
    replicates: 4
  - step_description: Cells were probed with lipofectamine 3000 to facilitate among.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 218
    replicates: 5
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      idea.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 22
    replicates: 5
control_groups:
- control_type: Vehicle Control
  description: Military seem keep note such than media wide yourself behind phone.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Stephen
  Marquez and results were consistent across multiple biological replicates.
