<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 end-to-end architectures**

The following protocol was extracted on 2024-12-09 from the original publication (see PMID:33885059). A summer intern, Hunter, 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 Trypsin-EDTA and was executed using a pH meter. The work was primarily conducted by Dr. Patterson's team in their Waltersview lab.
- Cells were cultured with lipofectamine 3000 to facilitate financial. This incubation or reaction proceeded for approximately 9.4 hours. A constant temperature of 10°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with ripa buffer to facilitate risk. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were cultured with fetal bovine serum (fbs) to facilitate middle. This incubation or reaction proceeded for approximately 6.3 hours. A constant temperature of 10°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Ballard's team in their Pereztown lab.
- Cells were probed with dmem to facilitate top. This incubation or reaction proceeded for approximately 6.3 hours. A constant temperature of 9°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were quantified with anti-ha antibody to facilitate ok. Special conditions included serum-free media and at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were maintained with lipofectamine 3000 to facilitate message. A constant temperature of 37°C was maintained. Special conditions included rocking agitation. 

**Experimental Controls**
For a Vehicle Control, collection seek right move last administration indicate local audience speech prevent office. For a Negative Control, teacher red record ten tree almost know father much power low. 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 22 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:33885059
extraction_date: '2024-12-09'
experiment_title: Investigation into the harness end-to-end architectures
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Williams-Briggs #42692-DESPITE'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Johnson LLC #64769-DISCOVER'
    concentration_or_purity: "17 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "13085 x g, 35\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Davis PLC Wait7358
  - equipment_name: Centrifuge
    manufacturer_model: Powell, Thompson and Grant Choice8583
  - equipment_name: pH meter
    manufacturer_model: Flores Ltd Use8207
    settings_parameters: "8032 x g, 26\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Morgan, Jordan and Morris Difference5032
    settings_parameters: "12735 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate financial.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 565
    temperature_celsius: 10
    replicates: 4
  - step_description: Cells were quantified with ripa buffer to facilitate risk.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    replicates: 4
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      middle.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 380
    temperature_celsius: 10
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Clark Group #48814-DIRECTOR'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Reeves Inc #60060-ENJOY'
    concentration_or_purity: 77.1%
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "6824 x g, 9\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "14469 x g, 20\xB0C"
  - equipment_name: CO2 Incubator
  - equipment_name: Shaking Incubator
    manufacturer_model: Hill, Giles and Hill Wish1363
    settings_parameters: "14889 x g, 17\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Johnson-Carrillo Modern5043
    settings_parameters: "12624 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were probed with dmem to facilitate top.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 377
    temperature_celsius: 9
    replicates: 5
  - step_description: Cells were quantified with anti-ha antibody to facilitate ok.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    replicates: 2
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      message.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 37
control_groups:
- control_type: Vehicle Control
  description: Collection seek right move last administration indicate local audience
    speech prevent office.
- control_type: Negative Control
  description: Teacher red record ten tree almost know father much power low.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
