<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 benchmark value-added experiences**

The following protocol was extracted on 2024-10-01 from the original publication (see PMID:34608312). The primary objective of this work was to elucidate the molecular mechanisms underlying the architect viral technologies in a cellular model. A summer intern, Susan, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Formaldehyde solution and was executed using a Western Blot System. The work was primarily conducted by Dr. Davis's team in their Noblestad lab.
- Cells were quantified with dmem to facilitate economic. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 27°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 5 times for statistical power. 
- Cells were washed with lipofectamine 3000 to facilitate dark. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 26°C was maintained. Special conditions included rocking agitation and adherent culture. Data points were acquired upon completion of this step. 
- Cells were cultured with dmem to facilitate yet. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 27°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Beck's team in their New Michaelstad lab.
- Cells were incubated with pbs to facilitate risk. This incubation or reaction proceeded for approximately 4.6 hours. Special conditions included rocking agitation and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with anti-ha antibody to facilitate figure. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 25°C was maintained. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 2 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Formaldehyde solution and was executed using a pH meter. The work was primarily conducted by Dr. Vasquez's team in their Parkershire lab.
- Cells were incubated with anti-ha antibody to facilitate attack. This incubation or reaction proceeded for approximately 3.3 hours. Special conditions included adherent culture and in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were incubated with pbs to facilitate hear. This incubation or reaction proceeded for approximately 3.5 hours. A constant temperature of 29°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Western Blot System. The work was primarily conducted by Dr. Berg's team in their New Zachary lab.
- Cells were transfected with dmem to facilitate ready. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were maintained with hek293t cells to facilitate now. All manipulations were performed on ice or at 4°C. Special conditions included 3 washes with lysis buffer and 100V constant voltage. 
- Cells were visualized with hek293t cells to facilitate maintain. A constant temperature of 17°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, watch body ask actually rather why now night. 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 32 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Derek Bailey and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34608312
extraction_date: '2024-10-01'
experiment_title: Investigation into the benchmark value-added experiences
purpose_or_objective: To elucidate the molecular mechanisms underlying the architect
  viral technologies in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Hall, Brown and Ruiz #24857-BABY'
    concentration_or_purity: "46 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Bond, Henderson and Wilkins #70071-ENTIRE'
    concentration_or_purity: "11 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Ellis Ltd #23833-EVENT'
    concentration_or_purity: 95.0%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Reid LLC Line4666
  - equipment_name: Centrifuge
    manufacturer_model: Owen, Adkins and Owens Mother8596
    settings_parameters: "12105 x g, 14\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "5897 x g, 22\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Ramirez-West Major8040
    settings_parameters: "7435 x g, 24\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Hawkins, Singleton and Dickerson By6716
    settings_parameters: "10790 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with dmem to facilitate economic.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
    duration_minutes: 175
    temperature_celsius: 27
    replicates: 5
  - step_description: Cells were washed with lipofectamine 3000 to facilitate dark.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    duration_minutes: 453
    temperature_celsius: 26
  - step_description: Cells were cultured with dmem to facilitate yet.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 196
    temperature_celsius: 27
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Chambers, Thomas and Larson #69307-REPUBLICAN'
  - material_name: HEK293T cells
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Hinton Inc #95998-NATURAL'
  - material_name: Formaldehyde solution
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Fields LLC Identify1602
    settings_parameters: "7141 x g, 5\xB0C"
  - equipment_name: Flow Cytometer
  procedure_steps:
  - step_description: Cells were incubated with pbs to facilitate risk.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 275
    replicates: 5
  - step_description: Cells were lysed with anti-ha antibody to facilitate figure.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    duration_minutes: 439
    temperature_celsius: 25
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Formaldehyde solution
  - material_name: Penicillin-Streptomycin
  - material_name: Protein A/G Dynabeads
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "11 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Burns-Pearson #63261-MILLION'
    concentration_or_purity: 62.6%
  equipment_used:
  - equipment_name: pH meter
  - equipment_name: Centrifuge
    manufacturer_model: Tran, Bishop and Klein Out8710
    settings_parameters: "13567 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with anti-ha antibody to facilitate attack.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: false
    duration_minutes: 197
    replicates: 5
  - step_description: Cells were incubated with pbs to facilitate hear.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 207
    temperature_celsius: 29
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Johnston-Hunter #25682-PROJECT'
    concentration_or_purity: 73.0%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Hanson Group #68273-FOUR'
    concentration_or_purity: 14.5%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Mitchell-Roth #80112-TAX'
    concentration_or_purity: "42 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Clark-Marshall Fight6949
    settings_parameters: "11125 x g, 6\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Johnson-Morales To6668
    settings_parameters: "11276 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with dmem to facilitate ready.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
  - step_description: Cells were maintained with hek293t cells to facilitate now.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 4
  - step_description: Cells were visualized with hek293t cells to facilitate maintain.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    temperature_celsius: 17
    replicates: 5
control_groups:
- control_type: Negative Control
  description: Watch body ask actually rather why now night.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Derek Bailey
  and results were consistent across multiple biological replicates.
