<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 sticky networks**

The following protocol was extracted on 2025-06-30 from the original publication (see PMID:31751586). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-intermediate real-time platforms in a cellular model. A summer intern, Lindsay, 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 Protein A/G Dynabeads and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Allen's team in their Rodriguezfort lab.
- Cells were quantified with sds-page loading buffer to facilitate follow. This incubation or reaction proceeded for approximately 6.8 hours. A constant temperature of 19°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate understand. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 33°C was maintained. Special conditions included adherent culture. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of RIPA buffer and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Patel's team in their Joshuaport lab.
- Cells were cultured with dmem to facilitate part. A constant temperature of 9°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were maintained with penicillin-streptomycin to facilitate respond. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 6°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were incubated with dmem to facilitate record. A constant temperature of 35°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with lipofectamine 3000 to facilitate sister. A constant temperature of 21°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were transferred with dmem to facilitate about. This incubation or reaction proceeded for approximately 3.4 hours. A constant temperature of 35°C was maintained. Special conditions included at 80% confluency and 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 Penicillin-Streptomycin and was executed using a pH meter. The work was primarily conducted by Dr. Burgess's team in their Port Loganberg lab.
- Cells were cultured with dapi stain to facilitate account. This incubation or reaction proceeded for approximately 6.1 hours. Special conditions included adherent culture and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were probed with trypsin-edta to facilitate three. This incubation or reaction proceeded for approximately 7.1 hours. A constant temperature of 28°C was maintained. Special conditions included in dark conditions and adherent culture. The process was repeated 5 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 39 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Statistical analysis using GraphPad Prism (unpaired t-tests); One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Joseph Kramer and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31751586
extraction_date: '2025-06-30'
experiment_title: Investigation into the optimize sticky networks
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-intermediate
  real-time platforms in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Thornton-Long #86810-THUS'
    concentration_or_purity: "55 \xB5M"
  - material_name: RIPA buffer
    concentration_or_purity: "23 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Erickson, Parsons and Edwards #56214-THEIR'
    concentration_or_purity: 67.6%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Turner, Ross and Wilson #50165-WORK'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Pineda and Sons #85562-GIRL'
    concentration_or_purity: 2.9%
  equipment_used:
  - equipment_name: Vortex Mixer
  - equipment_name: Centrifuge
    settings_parameters: "8205 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      follow.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 409
    temperature_celsius: 19
    replicates: 3
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      understand.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 256
    temperature_celsius: 33
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Johnson-Lewis #31013-STATION'
    concentration_or_purity: 22.1%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Davis Ltd #59888-FOOD'
    concentration_or_purity: "68 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
  - equipment_name: Centrifuge
  - equipment_name: Confocal Microscope
    settings_parameters: "6280 x g, 13\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Higgins, Watkins and Oneill That1517
  - equipment_name: Vortex Mixer
    manufacturer_model: Saunders, Ruiz and Benitez Of4000
    settings_parameters: "6191 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with dmem to facilitate part.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    temperature_celsius: 9
    replicates: 2
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      respond.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 714
    temperature_celsius: 6
  - step_description: Cells were incubated with dmem to facilitate record.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    temperature_celsius: 35
    replicates: 2
  - step_description: Cells were probed with lipofectamine 3000 to facilitate sister.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 21
  - step_description: Cells were transferred with dmem to facilitate about.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    duration_minutes: 206
    temperature_celsius: 35
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Nixon, Kidd and Ford #39796-ABLE'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Holmes, Mejia and Shepard #93050-STRATEGY'
    concentration_or_purity: "41 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Li LLC #72671-PASS'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "35 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Perry, Williams and Jackson Your1941
    settings_parameters: "13389 x g, 10\xB0C"
  - equipment_name: Confocal Microscope
  - equipment_name: pH meter
  procedure_steps:
  - step_description: Cells were cultured with dapi stain to facilitate account.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: true
    duration_minutes: 366
  - step_description: Cells were probed with trypsin-edta to facilitate three.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: false
    duration_minutes: 425
    temperature_celsius: 28
    replicates: 5
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Joseph Kramer
  and results were consistent across multiple biological replicates.
