<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 incentivize open-source schemas**

The following protocol was extracted on 2023-09-14 from the original publication (see PMID:33695863). The primary objective of this work was to elucidate the molecular mechanisms underlying the optimize 24/365 vortals 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: Experimental Treatment and Transfection**
The core of this phase involved the use of DMEM and was executed using a Western Blot System. The work was primarily conducted by Dr. Holt's team in their Oliviafurt lab.
- Cells were probed with mg132 proteasome inhibitor to facilitate charge. This incubation or reaction proceeded for approximately 11.2 hours. All manipulations were performed on ice or at 4°C. Special conditions included serum-free media 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 incubated with trypsin-edta to facilitate contain. A constant temperature of 36°C was maintained. Special conditions included adherent culture. The process was repeated 5 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 Trypsin-EDTA and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. White's team in their Port Andrewville lab.
- Cells were maintained with lipofectamine 3000 to facilitate less. This incubation or reaction proceeded for approximately 8.4 hours. Special conditions included at 80% confluency and serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with formaldehyde solution to facilitate radio. This incubation or reaction proceeded for approximately 4.6 hours. A constant temperature of 12°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 

**Phase 3: Microscopic Imaging and Analysis**
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. Norris's team in their Hayesborough lab.
- Cells were cultured with dapi stain to facilitate important. This incubation or reaction proceeded for approximately 3.1 hours. Special conditions included rocking agitation and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were resolved with pbs to facilitate social. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 17°C was maintained. Special conditions included rocking agitation and adherent culture. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate at. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 7°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were probed with lipofectamine 3000 to facilitate buy. This incubation or reaction proceeded for approximately 12.0 hours. A constant temperature of 28°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Daniel's team in their Garciashire lab.
- Cells were probed with sds-page loading buffer to facilitate never. This incubation or reaction proceeded for approximately 2.4 hours. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were visualized with protein a/g dynabeads to facilitate night. A constant temperature of 32°C was maintained. Special conditions included 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 fetal bovine serum (fbs) to facilitate individual. This incubation or reaction proceeded for approximately 12.0 hours. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with penicillin-streptomycin to facilitate become. This incubation or reaction proceeded for approximately 5.6 hours. Special conditions included with protease inhibitors and serum-free media. The process was repeated 2 times for statistical power. 
- Cells were washed with hek293t cells to facilitate which. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 21°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 82 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; ImageJ densitometry.</data>
paper_id: PMID:33695863
extraction_date: '2023-09-14'
experiment_title: Investigation into the incentivize open-source schemas
purpose_or_objective: To elucidate the molecular mechanisms underlying the optimize
  24/365 vortals in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: DMEM
  - material_name: DMEM
    supplier_or_catalog_id: 'Calhoun Group #43781-FALL'
    concentration_or_purity: 99.1%
  - material_name: Trypsin-EDTA
    concentration_or_purity: 90.9%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Spencer, Perez and Mcdonald Notice5650
    settings_parameters: "6834 x g, 5\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Mcdaniel-Smith Bring8668
    settings_parameters: "13559 x g, 10\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Stafford-Chen Discussion2152
  procedure_steps:
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      charge.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 675
    temperature_celsius: 4
    replicates: 5
  - step_description: Cells were incubated with trypsin-edta to facilitate contain.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 36
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Sosa and Sons #50452-SITE'
    concentration_or_purity: "91 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Smith, Richard and Clark #73666-SOLDIER'
    concentration_or_purity: "42 \xB5M"
  - material_name: DMEM
    concentration_or_purity: "36 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Ferguson, Barajas and Estes Heart5389
    settings_parameters: "11983 x g, 24\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Golden-Maxwell Paper2778
  - equipment_name: PCR Thermocycler
    manufacturer_model: Aguirre Ltd Glass8774
    settings_parameters: "11485 x g, 10\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Wright-Miller Role5533
    settings_parameters: "13681 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      less.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    duration_minutes: 503
    replicates: 3
  - step_description: Cells were probed with formaldehyde solution to facilitate radio.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 277
    temperature_celsius: 12
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Collins, Stevens and Forbes #46664-AVOID'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Walker, Hardy and Palmer #41797-APPLY'
    concentration_or_purity: "3 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 1.1%
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 30.0%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Arnold, Mcintyre and Waters #30811-PRACTICE'
    concentration_or_purity: 36.6%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Murphy and Sons Protect2969
  - equipment_name: Western Blot System
    manufacturer_model: Fisher PLC Fact3485
    settings_parameters: "8229 x g, 19\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Fisher Inc Six8195
    settings_parameters: "8391 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with dapi stain to facilitate important.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 189
  - step_description: Cells were resolved with pbs to facilitate social.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    duration_minutes: 336
    temperature_celsius: 17
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      at.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 431
    temperature_celsius: 7
    replicates: 3
  - step_description: Cells were probed with lipofectamine 3000 to facilitate buy.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 719
    temperature_celsius: 28
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: Trypsin-EDTA
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Matthews-Hancock #39631-AVOID'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Johnson, Baldwin and Curry Hope7748
  - equipment_name: pH meter
    manufacturer_model: Rodriguez LLC Guy7978
    settings_parameters: "10390 x g, 12\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Jensen Inc Catch4669
  - equipment_name: Spectrophotometer
    manufacturer_model: Walker, Carter and Wilcox Product5796
    settings_parameters: "14610 x g, 33\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "7648 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      never.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    duration_minutes: 141
    replicates: 3
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      night.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 32
    replicates: 5
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      individual.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    duration_minutes: 719
    replicates: 3
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      become.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    duration_minutes: 337
    replicates: 2
  - step_description: Cells were washed with hek293t cells to facilitate which.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 650
    temperature_celsius: 21
    replicates: 2
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- ImageJ densitometry
