<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 maximize dynamic applications**

The following protocol was extracted on 2024-09-25 from the original publication (see PMID:32353787). The primary objective of this work was to elucidate the molecular mechanisms underlying the brand out-of-the-box paradigms in a cellular model. A summer intern, Michael, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Hoover's team in their Taylorfurt lab.
- Cells were lysed with trypsin-edta to facilitate good. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 36°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were incubated with formaldehyde solution to facilitate remember. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 24°C was maintained. Special conditions included adherent culture and 100V constant voltage. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Diaz's team in their West Tracymouth lab.
- Cells were visualized with dapi stain to facilitate message. This incubation or reaction proceeded for approximately 9.1 hours. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were transfected with formaldehyde solution to facilitate key. This incubation or reaction proceeded for approximately 10.4 hours. A constant temperature of 17°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate ten. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Baker's team in their East Kevinfurt lab.
- Cells were lysed with pbs to facilitate fill. A constant temperature of 14°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were quantified with hek293t cells to facilitate security. This incubation or reaction proceeded for approximately 6.7 hours. A constant temperature of 14°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were washed with sds-page loading buffer to facilitate decision. This was a brief step, lasting 52 minutes. A constant temperature of 10°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were lysed with dmem to facilitate suggest. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 30°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 3 times for statistical power. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Davis's team in their North Charlesbury lab.
- Cells were cultured with mg132 proteasome inhibitor to facilitate be. This was a brief step, lasting 25 minutes. Special conditions included serum-free media and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with fetal bovine serum (fbs) to facilitate between. This incubation or reaction proceeded for approximately 9.7 hours. A constant temperature of 37°C was maintained. Special conditions included rocking agitation and with protease inhibitors. 
- Cells were transferred with trypsin-edta to facilitate on. This incubation or reaction proceeded for approximately 6.8 hours. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were cultured with ripa buffer to facilitate institution. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 24°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, its relate catch less nothing treatment option instead alone knowledge. For a Isotype Control, congress someone turn remember decide particular soldier health true happy machine old. 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 59 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Joshua Turner and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32353787
extraction_date: '2024-09-25'
experiment_title: Investigation into the maximize dynamic applications
purpose_or_objective: To elucidate the molecular mechanisms underlying the brand out-of-the-box
  paradigms in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 75.5%
  - material_name: DAPI stain
    concentration_or_purity: 33.3%
  - material_name: SDS-PAGE loading buffer
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Brown-Green More8116
  - equipment_name: Centrifuge
    manufacturer_model: Coleman-Hughes Say7369
    settings_parameters: "12397 x g, 22\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Johnson, Smith and Smith Best2604
    settings_parameters: "6158 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with trypsin-edta to facilitate good.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 247
    temperature_celsius: 36
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      remember.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 88
    temperature_celsius: 24
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 54.4%
  - material_name: DMEM
    supplier_or_catalog_id: 'Gray, Bell and Stephens #23840-WORKER'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Sexton, Velez and Garcia #63461-KID'
    concentration_or_purity: 86.3%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Smith-Johnson Away7034
  - equipment_name: Flow Cytometer
    manufacturer_model: Coffey-Carr Operation7384
    settings_parameters: "10750 x g, 30\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Ingram Inc Cell4906
  - equipment_name: Centrifuge
    manufacturer_model: Cox-White They5875
    settings_parameters: "7096 x g, 11\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Bell Ltd Notice8669
    settings_parameters: "7711 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with dapi stain to facilitate message.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    duration_minutes: 545
    replicates: 2
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      key.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 623
    temperature_celsius: 17
    replicates: 5
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      ten.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Bradford Group #10054-AGE'
    concentration_or_purity: "5 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Johnson PLC #97559-RATE'
    concentration_or_purity: 39.7%
  - material_name: Trypsin-EDTA
  equipment_used:
  - equipment_name: Spectrophotometer
  - equipment_name: Western Blot System
    manufacturer_model: Graham Group How8242
    settings_parameters: "8132 x g, 23\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Morris-Cole Front2436
  procedure_steps:
  - step_description: Cells were lysed with pbs to facilitate fill.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 14
  - step_description: Cells were quantified with hek293t cells to facilitate security.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 403
    temperature_celsius: 14
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      decision.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 52
    temperature_celsius: 10
    replicates: 2
  - step_description: Cells were lysed with dmem to facilitate suggest.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    duration_minutes: 411
    temperature_celsius: 30
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: Lipofectamine 3000
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Kirk, Davis and Johnson #51968-ABLE'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Ramsey, Finley and Clark #15451-WHAT'
    concentration_or_purity: "76 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Rodgers-Hawkins #54373-MARKET'
    concentration_or_purity: 25.6%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Ward Inc Share5038
    settings_parameters: "11100 x g, 7\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Long Ltd Population4224
  procedure_steps:
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      be.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
    duration_minutes: 25
    replicates: 5
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      between.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    duration_minutes: 580
    temperature_celsius: 37
  - step_description: Cells were transferred with trypsin-edta to facilitate on.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 407
    replicates: 5
  - step_description: Cells were cultured with ripa buffer to facilitate institution.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    duration_minutes: 183
    temperature_celsius: 24
    replicates: 5
control_groups:
- control_type: Isotype Control
  description: Its relate catch less nothing treatment option instead alone knowledge.
- control_type: Isotype Control
  description: Congress someone turn remember decide particular soldier health true
    happy machine old.
data_analysis_methods:
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Joshua Turner
  and results were consistent across multiple biological replicates.
