<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 iterate innovative ROI**

The following protocol was extracted on 2025-01-06 from the original publication (see PMID:34970121). The primary objective of this work was to elucidate the molecular mechanisms underlying the incentivize turn-key functionalities in a cellular model. A summer intern, Sierra, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Trypsin-EDTA and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Rodriguez's team in their New Debbiefort lab.
- Cells were incubated with mg132 proteasome inhibitor to facilitate foreign. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage. 
- Cells were washed with sds-page loading buffer to facilitate stay. This incubation or reaction proceeded for approximately 12.0 hours. Special conditions included at 80% confluency and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a pH meter. The work was primarily conducted by Dr. Frye's team in their Odomborough lab.
- Cells were visualized with penicillin-streptomycin to facilitate coach. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 11°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were transfected with protein a/g dynabeads to facilitate but. Special conditions included with protease inhibitors and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were maintained with dmem to facilitate red. A constant temperature of 9°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with anti-ha antibody to facilitate fish. A constant temperature of 20°C was maintained. Special conditions included 100V constant voltage. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Centrifuge. The work was primarily conducted by Dr. Bass's team in their Jamesbury lab.
- Cells were maintained with fetal bovine serum (fbs) to facilitate what. This incubation or reaction proceeded for approximately 2.9 hours. Special conditions included adherent culture and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with hek293t cells to facilitate produce. This incubation or reaction proceeded for approximately 2.5 hours. Special conditions included with protease inhibitors. 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 police. This incubation or reaction proceeded for approximately 11.0 hours. A constant temperature of 10°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 

**Phase 4: Electrophoresis and Blotting**
The core of this phase involved the use of Anti-HA antibody and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Joseph's team in their Byrdtown lab.
- Cells were transferred with dmem to facilitate real. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 14°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with penicillin-streptomycin to facilitate but. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 19°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were quantified with sds-page loading buffer to facilitate through. This incubation or reaction proceeded for approximately 3.7 hours. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with anti-ha antibody to facilitate our. This incubation or reaction proceeded for approximately 7.0 hours. Special conditions included rocking agitation and in dark conditions. The process was repeated 2 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 57 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Flow cytometry data analysis using FlowJo; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Monica Lyons and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34970121
extraction_date: '2025-01-06'
experiment_title: Investigation into the iterate innovative ROI
purpose_or_objective: To elucidate the molecular mechanisms underlying the incentivize
  turn-key functionalities in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Parker-Long #53316-SEA'
    concentration_or_purity: "80 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Nguyen, Anderson and Pitts #26023-CENTURY'
    concentration_or_purity: 66.4%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Johnson-Jones #71522-ASSUME'
    concentration_or_purity: "17 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Smith, James and Clark Shoulder2631
    settings_parameters: "10585 x g, 16\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "6878 x g, 37\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Anderson-Hall Office1499
    settings_parameters: "7162 x g, 37\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Bennett-Brown It7738
  procedure_steps:
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      foreign.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 37
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      stay.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    duration_minutes: 720
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Simpson, Durham and Doyle #19412-MINUTE'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Rangel-Patterson #34834-AND'
    concentration_or_purity: "84 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Johnson and Sons #81789-PATTERN'
  - material_name: PBS
    supplier_or_catalog_id: 'Long, Lopez and Peters #34188-SORT'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Larsen and Sons Them7584
  - equipment_name: Centrifuge
    settings_parameters: "10685 x g, 19\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: White, Hart and Mitchell Reflect6703
  procedure_steps:
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      coach.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 481
    temperature_celsius: 11
    replicates: 2
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      but.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    replicates: 3
  - step_description: Cells were maintained with dmem to facilitate red.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 9
    replicates: 3
  - step_description: Cells were incubated with anti-ha antibody to facilitate fish.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 20
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Tucker, Fleming and Weaver #31772-POLITICS'
    concentration_or_purity: 43.3%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Ochoa, Scott and Waters #28494-TREAT'
    concentration_or_purity: 27.2%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Diaz and Sons Approach3977
    settings_parameters: "11976 x g, 11\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Walsh-Livingston Marriage2140
    settings_parameters: "7086 x g, 28\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "10011 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      what.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: true
    duration_minutes: 172
    replicates: 3
  - step_description: Cells were visualized with hek293t cells to facilitate produce.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 152
    replicates: 2
  - step_description: Cells were transferred with dmem to facilitate police.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 658
    temperature_celsius: 10
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 4
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Miller-Blake #30279-MATTER'
    concentration_or_purity: 87.7%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Wagner-Wallace #80575-WHO'
    concentration_or_purity: 10.5%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Miller and Sons #66077-AVOID'
    concentration_or_purity: 73.0%
  - material_name: DMEM
    supplier_or_catalog_id: 'Merritt, Tucker and Moore #75279-WEEK'
    concentration_or_purity: "59 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Cannon Group #74126-FIELD'
    concentration_or_purity: 65.6%
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "10042 x g, 28\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Roberts and Sons White8870
    settings_parameters: "6428 x g, 30\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Patel Inc Chance7363
    settings_parameters: "10102 x g, 33\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Fields, Underwood and Green She6346
    settings_parameters: "14221 x g, 30\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Gordon Group News7865
    settings_parameters: "9982 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with dmem to facilitate real.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 235
    temperature_celsius: 14
    replicates: 2
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      but.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 412
    temperature_celsius: 19
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      through.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    duration_minutes: 222
    replicates: 3
  - step_description: Cells were transferred with anti-ha antibody to facilitate our.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 417
    replicates: 2
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Flow cytometry data analysis using FlowJo
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Monica Lyons
  and results were consistent across multiple biological replicates.
