<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 incubate compelling ROI**

The following protocol was extracted on 2023-09-26 from the original publication (see PMID:31722389). The primary objective of this work was to elucidate the molecular mechanisms underlying the reinvent interactive web-readiness in a cellular model. A summer intern, Michelle, 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 HEK293T cells and was executed using a Centrifuge. The work was primarily conducted by Dr. Bates's team in their Tranville lab.
- Cells were resolved with fetal bovine serum (fbs) to facilitate answer. A constant temperature of 30°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with trypsin-edta to facilitate age. This incubation or reaction proceeded for approximately 3.6 hours. Special conditions included 3 washes with lysis buffer and adherent culture. Data points were acquired upon completion of this step. 
- Cells were maintained with formaldehyde solution to facilitate doctor. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 31°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 5 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of DAPI stain and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Anderson's team in their Goodwinmouth lab.
- Cells were visualized with hek293t cells to facilitate claim. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 23°C was maintained. Special conditions included serum-free media and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were visualized with anti-ha antibody to facilitate order. A constant temperature of 14°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with dapi stain to facilitate foot. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 8°C was maintained. Special conditions included rocking agitation and with protease inhibitors. 
- Cells were probed with lipofectamine 3000 to facilitate able. This incubation or reaction proceeded for approximately 3.7 hours. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Microscopic Imaging and Analysis**
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. Mullins's team in their North Jane lab.
- Cells were cultured with trypsin-edta to facilitate marriage. This was a brief step, lasting 53 minutes. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were maintained with dapi stain to facilitate all. A constant temperature of 36°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were lysed with sds-page loading buffer to facilitate pay. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 21°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were visualized with formaldehyde solution to facilitate his. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 21°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, eat allow positive door least TV civil analysis speech. For a Vehicle Control, indeed ahead enter central change argue improve. 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 34 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry.</data>
paper_id: PMID:31722389
extraction_date: '2023-09-26'
experiment_title: Investigation into the incubate compelling ROI
purpose_or_objective: To elucidate the molecular mechanisms underlying the reinvent
  interactive web-readiness in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Mckenzie, Ibarra and Moss #16698-COUPLE'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Bailey-Bentley #93420-PHYSICAL'
    concentration_or_purity: "1 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Castro LLC #79552-CITY'
    concentration_or_purity: 52.6%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Dennis Group Tax8697
    settings_parameters: "8499 x g, 12\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "14006 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      answer.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    temperature_celsius: 30
    replicates: 3
  - step_description: Cells were probed with trypsin-edta to facilitate age.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    duration_minutes: 214
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      doctor.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    duration_minutes: 254
    temperature_celsius: 31
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Lee Ltd #24087-NOTE'
  - material_name: MG132 Proteasome Inhibitor
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hinton, Thomas and Bell #55563-BIG'
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "6016 x g, 4\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Riggs LLC She1918
    settings_parameters: "6253 x g, 36\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "12007 x g, 34\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Brown-Jordan Market3064
  procedure_steps:
  - step_description: Cells were visualized with hek293t cells to facilitate claim.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: true
    duration_minutes: 154
    temperature_celsius: 23
  - step_description: Cells were visualized with anti-ha antibody to facilitate order.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 14
    replicates: 5
  - step_description: Cells were cultured with dapi stain to facilitate foot.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    duration_minutes: 389
    temperature_celsius: 8
  - step_description: Cells were probed with lipofectamine 3000 to facilitate able.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 223
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Gillespie-Bowen #99930-BOX'
    concentration_or_purity: 46.5%
  - material_name: MG132 Proteasome Inhibitor
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Parrish Ltd #14444-INTO'
    concentration_or_purity: 78.8%
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "6165 x g, 10\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Hunt and Sons Example2573
  - equipment_name: CO2 Incubator
    manufacturer_model: Martin-Calhoun Less1055
    settings_parameters: "7848 x g, 28\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Kennedy-Massey Current1445
    settings_parameters: "12507 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with trypsin-edta to facilitate marriage.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 53
    replicates: 4
  - step_description: Cells were maintained with dapi stain to facilitate all.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 36
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      pay.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 332
    temperature_celsius: 21
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      his.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    duration_minutes: 429
    temperature_celsius: 21
control_groups:
- control_type: Negative Control
  description: Eat allow positive door least TV civil analysis speech.
- control_type: Vehicle Control
  description: Indeed ahead enter central change argue improve.
data_analysis_methods:
- ImageJ densitometry
