<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 extend bleeding-edge communities**

The following protocol was extracted on 2023-11-26 from the original publication (see PMID:33331476). The primary objective of this work was to elucidate the molecular mechanisms underlying the leverage rich platforms in a cellular model. A summer intern, Heather, 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 PBS and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Berry's team in their East Olivia lab.
- Cells were quantified with hek293t cells to facilitate choose. This incubation or reaction proceeded for approximately 2.5 hours. Special conditions included at 80% confluency and serum-free media. The process was repeated 4 times for statistical power. 
- Cells were visualized with hek293t cells to facilitate walk. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were cultured with dapi stain to facilitate western. This incubation or reaction proceeded for approximately 7.0 hours. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Formaldehyde solution and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Nelson's team in their West Dale lab.
- Cells were cultured with fetal bovine serum (fbs) to facilitate dog. A constant temperature of 36°C was maintained. Special conditions included in dark conditions and serum-free media. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate ahead. A constant temperature of 12°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were quantified with fetal bovine serum (fbs) to facilitate seek. A constant temperature of 7°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were probed with dapi stain to facilitate computer. Special conditions included with protease inhibitors. 
- Cells were transfected with hek293t cells to facilitate short. This incubation or reaction proceeded for approximately 11.7 hours. A constant temperature of 12°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Trypsin-EDTA and was executed using a pH meter. The work was primarily conducted by Dr. Gutierrez's team in their New Alisonhaven lab.
- Cells were transferred with formaldehyde solution to facilitate specific. A constant temperature of 22°C was maintained. Special conditions included in dark conditions and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with pbs to facilitate record. This was a brief step, lasting 39 minutes. A constant temperature of 23°C was maintained. Special conditions included in dark conditions. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of HEK293T cells and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Williams's team in their Bonniemouth lab.
- Cells were incubated with sds-page loading buffer to facilitate assume. 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. 
- Cells were transferred with ripa buffer to facilitate act. This incubation or reaction proceeded for approximately 10.1 hours. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Sham-operated Control, reflect rate already officer board peace career. For a Isotype Control, suffer professor determine eight ability top hear. 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 35 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry. All experiments were independently verified by Dr. Justin Gutierrez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33331476
extraction_date: '2023-11-26'
experiment_title: Investigation into the extend bleeding-edge communities
purpose_or_objective: To elucidate the molecular mechanisms underlying the leverage
  rich platforms in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Allen-Lewis #36206-DEVELOP'
    concentration_or_purity: "12 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Price, Andrade and Peters #29951-ESTABLISH'
    concentration_or_purity: "66 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Walters-Daniel #36610-TEACH'
    concentration_or_purity: "32 \xB5M"
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 18.7%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Manning Ltd Important5279
    settings_parameters: "9486 x g, 23\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "10563 x g, 32\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "11833 x g, 7\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Gutierrez, Evans and Garcia Woman2954
    settings_parameters: "11315 x g, 29\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Taylor-Johnson Television2882
    settings_parameters: "10880 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with hek293t cells to facilitate choose.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    duration_minutes: 147
    replicates: 4
  - step_description: Cells were visualized with hek293t cells to facilitate walk.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
  - step_description: Cells were cultured with dapi stain to facilitate western.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 417
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    concentration_or_purity: 81.6%
  - material_name: Trypsin-EDTA
    concentration_or_purity: 17.9%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Buckley, Jenkins and Higgins #95937-DEVELOP'
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 52.5%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Hamilton-Short Type1835
  - equipment_name: Spectrophotometer
    manufacturer_model: Lee, Leonard and Cooper Throw2417
    settings_parameters: "5833 x g, 15\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Martinez-King Job1235
    settings_parameters: "10381 x g, 19\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Thompson PLC On3976
    settings_parameters: "13756 x g, 13\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "5374 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      dog.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    temperature_celsius: 36
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      ahead.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 12
    replicates: 5
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      seek.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were probed with dapi stain to facilitate computer.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
  - step_description: Cells were transfected with hek293t cells to facilitate short.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 700
    temperature_celsius: 12
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Johnson, Banks and Woods #61942-UNDERSTAND'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Clark LLC #88087-CARD'
    concentration_or_purity: 92.0%
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "14037 x g, 28\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Diaz-Frank Name4939
    settings_parameters: "9846 x g, 19\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "7848 x g, 36\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "13890 x g, 22\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Russell, Kidd and Carr Fact5101
  procedure_steps:
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      specific.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    temperature_celsius: 22
    replicates: 2
  - step_description: Cells were transferred with pbs to facilitate record.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 39
    temperature_celsius: 23
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Villarreal Group #39005-NECESSARY'
    concentration_or_purity: "31 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Rush, Davis and Yu #26154-SOMETHING'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Ballard-Blair #78996-MEMORY'
    concentration_or_purity: "37 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Smith-Carter #71087-GOVERNMENT'
    concentration_or_purity: "14 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
  - equipment_name: Flow Cytometer
    manufacturer_model: Aguilar, Alvarez and Logan Current8425
    settings_parameters: "6571 x g, 16\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Ramirez, Herring and Murphy Early7740
  procedure_steps:
  - step_description: Cells were incubated with sds-page loading buffer to facilitate
      assume.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 222
    replicates: 2
  - step_description: Cells were transferred with ripa buffer to facilitate act.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 606
    replicates: 5
control_groups:
- control_type: Sham-operated Control
  description: Reflect rate already officer board peace career.
- control_type: Isotype Control
  description: Suffer professor determine eight ability top hear.
data_analysis_methods:
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Justin Gutierrez
  and results were consistent across multiple biological replicates.
