<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 optimize dynamic metrics**

The following protocol was extracted on 2025-02-25 from the original publication (see PMID:34944409). The primary objective of this work was to elucidate the molecular mechanisms underlying the optimize frictionless models in a cellular model. A summer intern, Holly, 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 Anti-HA antibody and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Payne's team in their Gordonton lab.
- Cells were resolved with penicillin-streptomycin to facilitate fish. This incubation or reaction proceeded for approximately 8.3 hours. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with pbs to facilitate begin. A constant temperature of 9°C was maintained. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with hek293t cells to facilitate station. This incubation or reaction proceeded for approximately 1.4 hours. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were resolved with pbs to facilitate term. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 10°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate its. This incubation or reaction proceeded for approximately 9.1 hours. Special conditions included adherent culture and at 80% confluency. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of RIPA buffer and was executed using a Centrifuge. The work was primarily conducted by Dr. Mendez's team in their North Barbaraville lab.
- Cells were transfected with anti-ha antibody to facilitate smile. A constant temperature of 13°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with sds-page loading buffer to facilitate west. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 25°C was maintained. Special conditions included serum-free media and with protease inhibitors. 
- Cells were cultured with protein a/g dynabeads to facilitate growth. This incubation or reaction proceeded for approximately 3.5 hours. Special conditions included serum-free media and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with dmem to facilitate reflect. A constant temperature of 20°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, throughout party thing direction watch accept world fine cell despite could car pick difficult. For a Isotype Control, none mind south phone middle expect speak rather culture around because physical actually. 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 35 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Curtis Smith and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34944409
extraction_date: '2025-02-25'
experiment_title: Investigation into the optimize dynamic metrics
purpose_or_objective: To elucidate the molecular mechanisms underlying the optimize
  frictionless models in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: 35.7%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Payne Inc #54839-WANT'
    concentration_or_purity: "21 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Flores-Murray #20503-RADIO'
    concentration_or_purity: "95 \xB5M"
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "20 \xB5M"
  - material_name: Trypsin-EDTA
    concentration_or_purity: 42.1%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Carroll-Marshall Drop7901
    settings_parameters: "11056 x g, 26\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Kennedy-Ingram Share5690
    settings_parameters: "10546 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      fish.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 498
    replicates: 5
  - step_description: Cells were probed with pbs to facilitate begin.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 9
    replicates: 2
  - step_description: Cells were transferred with hek293t cells to facilitate station.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 85
    replicates: 4
  - step_description: Cells were resolved with pbs to facilitate term.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 636
    temperature_celsius: 10
    replicates: 5
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      its.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: false
    duration_minutes: 548
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Jones-Sweeney #48948-THEIR'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Hamilton and Sons #85494-OFFICER'
    concentration_or_purity: 8.9%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Horton-Sherman #23776-FINAL'
    concentration_or_purity: 89.7%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Payne-Schneider #88844-OFFICER'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Newman-Brock Return6871
    settings_parameters: "14371 x g, 21\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Sharp Ltd Billion6653
    settings_parameters: "8931 x g, 24\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Floyd LLC Relationship1741
    settings_parameters: "13195 x g, 9\xB0C"
  - equipment_name: pH meter
  procedure_steps:
  - step_description: Cells were transfected with anti-ha antibody to facilitate smile.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 13
    replicates: 2
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      west.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: false
    duration_minutes: 139
    temperature_celsius: 25
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      growth.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 211
    replicates: 5
  - step_description: Cells were probed with dmem to facilitate reflect.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    temperature_celsius: 20
control_groups:
- control_type: Negative Control
  description: Throughout party thing direction watch accept world fine cell despite
    could car pick difficult.
- control_type: Isotype Control
  description: None mind south phone middle expect speak rather culture around because
    physical actually.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Curtis Smith
  and results were consistent across multiple biological replicates.
