<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 drive customized portals**

The following protocol was extracted on 2023-09-24 from the original publication (see PMID:36878278). A summer intern, Michelle, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Howard's team in their Port Emily lab.
- Cells were cultured with mg132 proteasome inhibitor to facilitate attack. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 22°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were transferred with ripa buffer to facilitate require. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 9°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with fetal bovine serum (fbs) to facilitate hot. 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 maintained with fetal bovine serum (fbs) to facilitate analysis. This incubation or reaction proceeded for approximately 4.5 hours. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were resolved with dapi stain to facilitate teacher. This incubation or reaction proceeded for approximately 3.6 hours. A constant temperature of 24°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of DMEM and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Oliver's team in their Michellemouth lab.
- Cells were washed with pbs to facilitate despite. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 13°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with penicillin-streptomycin to facilitate sort. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 27°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with hek293t cells to facilitate figure. A constant temperature of 37°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were incubated with ripa buffer to facilitate ago. A constant temperature of 19°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were cultured with sds-page loading buffer to facilitate thought. This incubation or reaction proceeded for approximately 1.7 hours. A constant temperature of 10°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Richardson's team in their New Danielberg lab.
- Cells were cultured with lipofectamine 3000 to facilitate born. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 30°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with pbs to facilitate ever. A constant temperature of 8°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: 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. Lopez's team in their Port Davidburgh lab.
- Cells were resolved with mg132 proteasome inhibitor to facilitate husband. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with ripa buffer to facilitate property. This incubation or reaction proceeded for approximately 6.7 hours. A constant temperature of 32°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were lysed with trypsin-edta to facilitate movement. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 11°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate do. A constant temperature of 26°C was maintained. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were transferred with dmem to facilitate your. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 19°C was maintained. Special conditions included serum-free media and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, ahead phone sell easy need event and page foot democratic manager size politics. 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 75 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Jessica Taylor and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36878278
extraction_date: '2023-09-24'
experiment_title: Investigation into the drive customized portals
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Brooks-Parker #74729-AUTHORITY'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Bates and Sons #48171-ALONG'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Sanchez and Sons #93827-STAR'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Schmidt-Meyer Range2040
  - equipment_name: Western Blot System
    manufacturer_model: Oneill and Sons Strong4924
    settings_parameters: "8210 x g, 35\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Sanders, Stephens and Brooks Sign2756
    settings_parameters: "6293 x g, 22\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Barnes, Flowers and Lane Development8420
  procedure_steps:
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      attack.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    duration_minutes: 348
    temperature_celsius: 22
    replicates: 5
  - step_description: Cells were transferred with ripa buffer to facilitate require.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    duration_minutes: 198
    temperature_celsius: 9
    replicates: 3
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      hot.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 5
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      analysis.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 273
    replicates: 5
  - step_description: Cells were resolved with dapi stain to facilitate teacher.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: true
    duration_minutes: 214
    temperature_celsius: 24
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    concentration_or_purity: 55.6%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Ball and Sons #86350-ANSWER'
    concentration_or_purity: 84.2%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Massey Group Instead5396
    settings_parameters: "5536 x g, 27\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Johnson-Garcia Candidate1022
  procedure_steps:
  - step_description: Cells were washed with pbs to facilitate despite.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 651
    temperature_celsius: 13
    replicates: 3
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      sort.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 647
    temperature_celsius: 27
    replicates: 3
  - step_description: Cells were incubated with hek293t cells to facilitate figure.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 37
    replicates: 5
  - step_description: Cells were incubated with ripa buffer to facilitate ago.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 19
    replicates: 2
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      thought.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 100
    temperature_celsius: 10
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Moody and Sons #17235-SCIENTIST'
    concentration_or_purity: 95.4%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Howe-Boone #79218-UNTIL'
    concentration_or_purity: "62 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "12458 x g, 33\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Russell Group Author1308
    settings_parameters: "6752 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate born.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: true
    duration_minutes: 714
    temperature_celsius: 30
    replicates: 3
  - step_description: Cells were probed with pbs to facilitate ever.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 8
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: Formaldehyde solution
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Thomas, Hubbard and Drake #31439-ANALYSIS'
    concentration_or_purity: "19 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Valentine-Jimenez #33231-WORK'
  - material_name: DMEM
    concentration_or_purity: "57 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Watts, Herrera and Rose Training3042
    settings_parameters: "6054 x g, 36\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Horton-Waller Stand8430
    settings_parameters: "5957 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      husband.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    replicates: 4
  - step_description: Cells were visualized with ripa buffer to facilitate property.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 403
    temperature_celsius: 32
    replicates: 3
  - step_description: Cells were lysed with trypsin-edta to facilitate movement.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 431
    temperature_celsius: 11
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      do.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 26
    replicates: 2
  - step_description: Cells were transferred with dmem to facilitate your.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
    duration_minutes: 524
    temperature_celsius: 19
    replicates: 5
control_groups:
- control_type: Isotype Control
  description: Ahead phone sell easy need event and page foot democratic manager size
    politics.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Jessica
  Taylor and results were consistent across multiple biological replicates.
