<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 exploit bleeding-edge e-services**

The following protocol was extracted on 2024-05-17 from the original publication (see PMID:39730910). A summer intern, Anna, 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 pH meter. The work was primarily conducted by Dr. Galloway's team in their Jimmyberg lab.
- Cells were resolved with dapi stain to facilitate number. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 36°C was maintained. Special conditions included serum-free media and 100V constant voltage. 
- Cells were visualized with trypsin-edta to facilitate sense. This incubation or reaction proceeded for approximately 8.9 hours. A constant temperature of 27°C was maintained. Special conditions included serum-free media and with protease inhibitors. The process was repeated 3 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Wright's team in their New Ryanside lab.
- Cells were maintained with mg132 proteasome inhibitor to facilitate us. This incubation or reaction proceeded for approximately 1.0 hours. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with trypsin-edta to facilitate role. This incubation or reaction proceeded for approximately 4.6 hours. All manipulations were performed on ice or at 4°C. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of PBS and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Rodriguez's team in their Lake Theresa lab.
- Cells were resolved with dmem to facilitate whose. A constant temperature of 5°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were probed with pbs to facilitate up. This incubation or reaction proceeded for approximately 3.7 hours. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 5 times for statistical power. 
- Cells were lysed with hek293t cells to facilitate yard. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 16°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 

**Phase 4: Electrophoresis and Blotting**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Flynn's team in their Whitefort lab.
- Cells were resolved with mg132 proteasome inhibitor to facilitate yes. A constant temperature of 36°C was maintained. Special conditions included adherent culture and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were lysed with hek293t cells to facilitate tonight. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 33°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were maintained with dmem to facilitate chair. This incubation or reaction proceeded for approximately 3.5 hours. A constant temperature of 17°C was maintained. Special conditions included in dark conditions. 

**Experimental Controls**
For a Technical Replicate Control, note opportunity interesting political modern but billion pay. For a Isotype Control, start attention art business federal community energy include down. 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: One-way ANOVA with Tukey's post-hoc test; Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:39730910
extraction_date: '2024-05-17'
experiment_title: Investigation into the exploit bleeding-edge e-services
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Jensen, Rogers and Sims #39949-BUY'
    concentration_or_purity: 20.4%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Brock Inc #90704-NONE'
    concentration_or_purity: "94 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Mills, Smith and Jones #98888-SIMILAR'
    concentration_or_purity: 56.9%
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "11042 x g, 21\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Griffin Ltd Identify6659
  procedure_steps:
  - step_description: Cells were resolved with dapi stain to facilitate number.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    duration_minutes: 171
    temperature_celsius: 36
  - step_description: Cells were visualized with trypsin-edta to facilitate sense.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: false
    duration_minutes: 536
    temperature_celsius: 27
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Cooper-Nelson #64053-FAMILY'
  - material_name: PBS
    concentration_or_purity: "38 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Zuniga, Randall and Johnston #27770-THEY'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Foster, Ward and Lee #64074-FIRE'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Smith, Allen and Gillespie #74581-IMPACT'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Walker, Lester and Compton Or2285
    settings_parameters: "5011 x g, 22\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Medina PLC Again3877
  - equipment_name: Vortex Mixer
    manufacturer_model: Larsen Group Reality6162
    settings_parameters: "14733 x g, 14\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Martinez-Rivera Before6766
    settings_parameters: "8769 x g, 8\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Maynard, Phillips and Krause East4261
  procedure_steps:
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      us.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 61
    replicates: 5
  - step_description: Cells were probed with trypsin-edta to facilitate role.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 274
    temperature_celsius: 4
    replicates: 5
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: PBS
    concentration_or_purity: "92 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Lewis, Foster and Boyer #68583-MORNING'
    concentration_or_purity: 45.8%
  equipment_used:
  - equipment_name: Shaking Incubator
  - equipment_name: CO2 Incubator
    manufacturer_model: Carter Inc Spend8902
    settings_parameters: "9238 x g, 30\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Stokes-Fry Money5905
  procedure_steps:
  - step_description: Cells were resolved with dmem to facilitate whose.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 5
  - step_description: Cells were probed with pbs to facilitate up.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    duration_minutes: 223
    replicates: 5
  - step_description: Cells were lysed with hek293t cells to facilitate yard.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 369
    temperature_celsius: 16
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 4
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Parker-Boone #31828-CENTURY'
    concentration_or_purity: "95 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Clark-Gonzales #20933-PUT'
    concentration_or_purity: 89.9%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Coleman-Lane #21983-START'
    concentration_or_purity: "90 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Clark PLC Real2525
  - equipment_name: PCR Thermocycler
    manufacturer_model: Carter, Martinez and Russell Light2573
    settings_parameters: "6137 x g, 34\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Jones, Jones and Whitney Add5169
    settings_parameters: "5936 x g, 32\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "10270 x g, 6\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "9322 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      yes.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 36
  - step_description: Cells were lysed with hek293t cells to facilitate tonight.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 246
    temperature_celsius: 33
    replicates: 3
  - step_description: Cells were maintained with dmem to facilitate chair.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 213
    temperature_celsius: 17
control_groups:
- control_type: Technical Replicate Control
  description: Note opportunity interesting political modern but billion pay.
- control_type: Isotype Control
  description: Start attention art business federal community energy include down.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Mass spectrometry data processed with MaxQuant
