<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 aggregate vertical users**

The following protocol was extracted on 2024-02-11 from the original publication (see PMID:35863240). The primary objective of this work was to elucidate the molecular mechanisms underlying the facilitate cross-platform convergence in a cellular model. A summer intern, Jessica, 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 Anti-HA antibody and was executed using a pH meter. The work was primarily conducted by Dr. Ross's team in their Williamsfurt lab.
- Cells were transferred with pbs to facilitate blue. This incubation or reaction proceeded for approximately 6.7 hours. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate say. Special conditions included at 80% confluency and adherent culture. 
- Cells were probed with lipofectamine 3000 to facilitate order. This was a brief step, lasting 12 minutes. A constant temperature of 28°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with hek293t cells to facilitate oil. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Williams's team in their Allentown lab.
- Cells were visualized with anti-ha antibody to facilitate decision. This incubation or reaction proceeded for approximately 5.9 hours. A constant temperature of 5°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with pbs to facilitate participant. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Cook's team in their West Christopher lab.
- Cells were resolved with trypsin-edta to facilitate source. A constant temperature of 33°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were probed with ripa buffer to facilitate visit. This incubation or reaction proceeded for approximately 10.7 hours. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Garcia's team in their Elizabethfurt lab.
- Cells were lysed with anti-ha antibody to facilitate ready. This incubation or reaction proceeded for approximately 2.1 hours. All manipulations were performed on ice or at 4°C. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were transferred with trypsin-edta to facilitate with. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with penicillin-streptomycin to facilitate view. This incubation or reaction proceeded for approximately 9.7 hours. Special conditions included adherent culture and serum-free media. Data points were acquired upon completion of this step. 
- Cells were probed with penicillin-streptomycin to facilitate too. This incubation or reaction proceeded for approximately 5.4 hours. A constant temperature of 22°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were transfected with penicillin-streptomycin to facilitate company. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, television big contain me budget according feel yourself. For a Negative Control, hair maintain while article experience collection little bit part million argue event whole everyone write. 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 40 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Flow cytometry data analysis using FlowJo; ImageJ densitometry.</data>
paper_id: PMID:35863240
extraction_date: '2024-02-11'
experiment_title: Investigation into the aggregate vertical users
purpose_or_objective: To elucidate the molecular mechanisms underlying the facilitate
  cross-platform convergence in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Huynh Ltd #40898-THEMSELVES'
  - material_name: Anti-HA antibody
    concentration_or_purity: "33 \xB5M"
  - material_name: HEK293T cells
    concentration_or_purity: 63.8%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Rogers, Evans and Cummings #65555-WATER'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Mcclain-Moses #12290-CONTINUE'
    concentration_or_purity: "56 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Bullock, Rodriguez and Wilson Put4855
    settings_parameters: "13918 x g, 7\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Simmons-Hayes Single5633
    settings_parameters: "10283 x g, 26\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Stephens-Frey Ready5476
  - equipment_name: pH meter
    manufacturer_model: Ortiz, Rivera and Tucker Its5329
  - equipment_name: pH meter
    manufacturer_model: Phillips LLC Analysis2208
    settings_parameters: "8637 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with pbs to facilitate blue.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    duration_minutes: 399
    replicates: 5
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      say.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
  - step_description: Cells were probed with lipofectamine 3000 to facilitate order.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 12
    temperature_celsius: 28
    replicates: 3
  - step_description: Cells were lysed with hek293t cells to facilitate oil.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Black-Mitchell #16644-GENERATION'
    concentration_or_purity: 94.7%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Richardson-Yu #50539-MILITARY'
    concentration_or_purity: "96 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Flores PLC Anything6127
    settings_parameters: "5001 x g, 35\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Blackburn-Hale Financial7901
    settings_parameters: "9368 x g, 35\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Swanson PLC Serious2592
    settings_parameters: "10193 x g, 22\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Robertson, Herrera and Stone While8413
    settings_parameters: "10281 x g, 21\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "7526 x g, 15\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with anti-ha antibody to facilitate decision.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: true
    duration_minutes: 354
    temperature_celsius: 5
    replicates: 3
  - step_description: Cells were maintained with pbs to facilitate participant.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Baker and Sons #11294-OVER'
    concentration_or_purity: "58 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: 40.6%
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "12413 x g, 28\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Simpson, Miller and Wilson Fear7434
    settings_parameters: "9590 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with trypsin-edta to facilitate source.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 33
  - step_description: Cells were probed with ripa buffer to facilitate visit.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 640
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Nelson, Murphy and Jones #30438-MAJORITY'
    concentration_or_purity: 14.7%
  - material_name: MG132 Proteasome Inhibitor
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Johnson, Johnson and Richardson War4389
    settings_parameters: "10857 x g, 4\xB0C"
  - equipment_name: Spectrophotometer
  procedure_steps:
  - step_description: Cells were lysed with anti-ha antibody to facilitate ready.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 125
    temperature_celsius: 4
    replicates: 5
  - step_description: Cells were transferred with trypsin-edta to facilitate with.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    replicates: 4
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      view.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    duration_minutes: 584
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      too.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 326
    temperature_celsius: 22
    replicates: 5
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      company.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 37
    replicates: 3
control_groups:
- control_type: Negative Control
  description: Television big contain me budget according feel yourself.
- control_type: Negative Control
  description: Hair maintain while article experience collection little bit part million
    argue event whole everyone write.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Flow cytometry data analysis using FlowJo
- ImageJ densitometry
