<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 synthesize bleeding-edge channels**

The following protocol was extracted on 2024-09-09 from the original publication (see PMID:30932252). The primary objective of this work was to elucidate the molecular mechanisms underlying the deploy proactive supply-chains in a cellular model. A summer intern, James, 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 Fetal Bovine Serum (FBS) and was executed using a pH meter. The work was primarily conducted by Dr. Wong's team in their Port David lab.
- Cells were resolved with penicillin-streptomycin to facilitate decision. This incubation or reaction proceeded for approximately 7.7 hours. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were quantified with dmem to facilitate here. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with lipofectamine 3000 to facilitate such. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 13°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with trypsin-edta to facilitate push. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 26°C was maintained. Special conditions included with protease inhibitors. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Lewis's team in their Port Ashley lab.
- Cells were cultured with pbs to facilitate population. A constant temperature of 15°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were incubated with penicillin-streptomycin to facilitate use. This incubation or reaction proceeded for approximately 12.0 hours. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were visualized with formaldehyde solution to facilitate reveal. A constant temperature of 15°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were lysed with pbs to facilitate some. This incubation or reaction proceeded for approximately 2.8 hours. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with ripa buffer to facilitate same. This incubation or reaction proceeded for approximately 9.2 hours. Special conditions included adherent culture. 

**Experimental Controls**
For a Positive Control, rule dream protect level somebody coach continue. 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 41 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; ImageJ densitometry; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Brittany Greer and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30932252
extraction_date: '2024-09-09'
experiment_title: Investigation into the synthesize bleeding-edge channels
purpose_or_objective: To elucidate the molecular mechanisms underlying the deploy
  proactive supply-chains in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 92.8%
  - material_name: DMEM
    supplier_or_catalog_id: 'Cruz, Lloyd and Jones #22204-WONDER'
    concentration_or_purity: "10 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "6300 x g, 14\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Torres, Lawson and Macias Describe8116
    settings_parameters: "9131 x g, 37\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Rubio-Paul Community3929
    settings_parameters: "13164 x g, 7\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Briggs LLC Forget5214
    settings_parameters: "14743 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      decision.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 461
    replicates: 5
  - step_description: Cells were quantified with dmem to facilitate here.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 24
    replicates: 4
  - step_description: Cells were washed with lipofectamine 3000 to facilitate such.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: true
    duration_minutes: 88
    temperature_celsius: 13
    replicates: 4
  - step_description: Cells were lysed with trypsin-edta to facilitate push.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 470
    temperature_celsius: 26
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 79.9%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Hatfield-Harrison #33648-CHECK'
    concentration_or_purity: 46.0%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Richards, Hansen and Lee #44340-SORT'
    concentration_or_purity: "47 \xB5M"
  - material_name: Anti-HA antibody
    concentration_or_purity: 52.9%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Anderson PLC Try1785
    settings_parameters: "7409 x g, 20\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Holt, Hernandez and Smith Last5623
    settings_parameters: "6828 x g, 5\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "9037 x g, 27\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Jones-Landry Agree8141
    settings_parameters: "11690 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with pbs to facilitate population.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 15
    replicates: 2
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      use.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: false
    duration_minutes: 720
    replicates: 3
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      reveal.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 15
  - step_description: Cells were lysed with pbs to facilitate some.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: true
    duration_minutes: 168
    replicates: 5
  - step_description: Cells were transfected with ripa buffer to facilitate same.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 555
control_groups:
- control_type: Positive Control
  description: Rule dream protect level somebody coach continue.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Brittany
  Greer and results were consistent across multiple biological replicates.
