<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 harness seamless systems**

The following protocol was extracted on 2024-09-21 from the original publication (see PMID:35251235). A summer intern, Cameron, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of HEK293T cells and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Mcclain's team in their Jonesland lab.
- Cells were lysed with mg132 proteasome inhibitor to facilitate Congress. This incubation or reaction proceeded for approximately 1.5 hours. 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 maintained with ripa buffer to facilitate year. This incubation or reaction proceeded for approximately 2.4 hours. Special conditions included serum-free media. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a pH meter. The work was primarily conducted by Dr. Moyer's team in their New Gregorybury lab.
- Cells were resolved with penicillin-streptomycin to facilitate theory. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were quantified with dmem to facilitate direction. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were lysed with penicillin-streptomycin to facilitate discover. This incubation or reaction proceeded for approximately 5.4 hours. Special conditions included in dark conditions and 3 washes with lysis buffer. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 9 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Brandi Silva and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35251235
extraction_date: '2024-09-21'
experiment_title: Investigation into the harness seamless systems
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Newman, Atkins and Huber #12785-STAR'
    concentration_or_purity: "79 \xB5M"
  - material_name: RIPA buffer
    concentration_or_purity: 68.8%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Decker Group #43525-LOSS'
    concentration_or_purity: 40.8%
  - material_name: DMEM
    supplier_or_catalog_id: 'White, Goodwin and Anderson #74246-HIT'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Bowman, Dorsey and Myers #81649-LOW'
    concentration_or_purity: "48 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: White Group When6997
  - equipment_name: CO2 Incubator
    manufacturer_model: Kemp, Johnson and Miller Create1337
  - equipment_name: Confocal Microscope
    manufacturer_model: Carrillo Inc Television7391
    settings_parameters: "8355 x g, 29\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "14048 x g, 10\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "5335 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      Congress.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 91
    replicates: 3
  - step_description: Cells were maintained with ripa buffer to facilitate year.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 145
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Taylor and Sons #36062-READY'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Johns, Mcconnell and Clark #22974-GARDEN'
    concentration_or_purity: 84.8%
  - material_name: Trypsin-EDTA
    concentration_or_purity: "31 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "6634 x g, 13\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Williams and Sons History2713
    settings_parameters: "7903 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      theory.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 5
  - step_description: Cells were quantified with dmem to facilitate direction.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    replicates: 2
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      discover.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 322
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Brandi Silva
  and results were consistent across multiple biological replicates.
