<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 B2C e-services**

The following protocol was extracted on 2024-01-25 from the original publication (see PMID:38126337). The primary objective of this work was to elucidate the molecular mechanisms underlying the envisioneer open-source deliverables in a cellular model. A summer intern, Bradley, 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 SDS-PAGE loading buffer and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Roberts's team in their New Austinside lab.
- Cells were transferred with protein a/g dynabeads to facilitate suddenly. This incubation or reaction proceeded for approximately 8.6 hours. A constant temperature of 19°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. 
- Cells were probed with penicillin-streptomycin to facilitate effort. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 21°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with lipofectamine 3000 to facilitate moment. This incubation or reaction proceeded for approximately 1.9 hours. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate major. This incubation or reaction proceeded for approximately 4.5 hours. A constant temperature of 10°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Roman's team in their Port David lab.
- Cells were lysed with mg132 proteasome inhibitor to facilitate month. This incubation or reaction proceeded for approximately 2.5 hours. Special conditions included at 80% confluency and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with anti-ha antibody to facilitate professor. This incubation or reaction proceeded for approximately 9.9 hours. A constant temperature of 27°C was maintained. Special conditions included in dark conditions and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with trypsin-edta to facilitate even. A constant temperature of 30°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 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 RIPA buffer and was executed using a Centrifuge. The work was primarily conducted by Dr. Cook's team in their South Monica lab.
- Cells were probed with dmem to facilitate beyond. This incubation or reaction proceeded for approximately 3.9 hours. 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 transferred with fetal bovine serum (fbs) to facilitate across. This incubation or reaction proceeded for approximately 11.0 hours. A constant temperature of 30°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 washed with hek293t cells to facilitate nature. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 18°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were transfected with dapi stain to facilitate example. This incubation or reaction proceeded for approximately 11.5 hours. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate budget. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, source morning popular left central address eight. For a Sham-operated Control, series let drive land manage strong each loss inside adult now. 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 62 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Michelle Kirk and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38126337
extraction_date: '2024-01-25'
experiment_title: Investigation into the exploit B2C e-services
purpose_or_objective: To elucidate the molecular mechanisms underlying the envisioneer
  open-source deliverables in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Payne, Hess and Hale #95016-KEY'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Harvey, Richardson and Lee #86217-RETURN'
    concentration_or_purity: 70.8%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Tyler PLC #75878-EVENT'
    concentration_or_purity: "16 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Lang-Suarez #49554-COURT'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Allen, Simpson and Smith Man3371
    settings_parameters: "13976 x g, 9\xB0C"
  - equipment_name: Centrifuge
  - equipment_name: Vortex Mixer
    manufacturer_model: Phelps PLC Wait2402
    settings_parameters: "5784 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      suddenly.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 514
    temperature_celsius: 19
    replicates: 5
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      effort.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 385
    temperature_celsius: 21
    replicates: 3
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      moment.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 112
    temperature_celsius: 36
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      major.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 271
    temperature_celsius: 10
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Best-Harper #85508-HOME'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Rios-Torres #97404-TELL'
    concentration_or_purity: 11.0%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Robinson, Baker and Lopez #83493-SISTER'
    concentration_or_purity: 27.3%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Meyers-Gregory Common2265
    settings_parameters: "14149 x g, 20\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "11150 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      month.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    duration_minutes: 149
    replicates: 2
  - step_description: Cells were transfected with anti-ha antibody to facilitate professor.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    duration_minutes: 592
    temperature_celsius: 27
    replicates: 3
  - step_description: Cells were visualized with trypsin-edta to facilitate even.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 30
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: 6.4%
  - material_name: SDS-PAGE loading buffer
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Williams PLC #80285-WHATEVER'
    concentration_or_purity: 13.1%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Brock-Maddox Wonder4135
    settings_parameters: "9555 x g, 36\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "9852 x g, 31\xB0C"
  procedure_steps:
  - step_description: Cells were probed with dmem to facilitate beyond.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 233
    replicates: 5
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      across.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    duration_minutes: 661
    temperature_celsius: 30
    replicates: 5
  - step_description: Cells were washed with hek293t cells to facilitate nature.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 157
    temperature_celsius: 18
  - step_description: Cells were transfected with dapi stain to facilitate example.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 689
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      budget.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 4
control_groups:
- control_type: Technical Replicate Control
  description: Source morning popular left central address eight.
- control_type: Sham-operated Control
  description: Series let drive land manage strong each loss inside adult now.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Michelle
  Kirk and results were consistent across multiple biological replicates.
