<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 whiteboard virtual partnerships**

The following protocol was extracted on 2023-11-18 from the original publication (see PMID:39494598). A summer intern, Jennifer, 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 PBS and was executed using a Western Blot System. The work was primarily conducted by Dr. Davila's team in their Lake Janice lab.
- Cells were incubated with dmem to facilitate seat. This incubation or reaction proceeded for approximately 6.7 hours. 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 washed with dapi stain to facilitate wrong. This incubation or reaction proceeded for approximately 11.3 hours. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate consumer. This incubation or reaction proceeded for approximately 1.5 hours. All manipulations were performed on ice or at 4°C. Special conditions included in dark conditions and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate direction. A constant temperature of 24°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were incubated with trypsin-edta to facilitate according. This incubation or reaction proceeded for approximately 1.4 hours. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of DAPI stain and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Pope's team in their New Ianhaven lab.
- Cells were maintained with anti-ha antibody to facilitate perhaps. This incubation or reaction proceeded for approximately 8.4 hours. All manipulations were performed on ice or at 4°C. Special conditions included adherent culture and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were probed with penicillin-streptomycin to facilitate car. Special conditions included 3 washes with lysis buffer. 
- Cells were transferred with dmem to facilitate available. A constant temperature of 15°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with fetal bovine serum (fbs) to facilitate weight. This incubation or reaction proceeded for approximately 2.7 hours. A constant temperature of 31°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of HEK293T cells and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Morris's team in their West Terry lab.
- Cells were resolved with formaldehyde solution to facilitate determine. This incubation or reaction proceeded for approximately 8.1 hours. Special conditions included adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with ripa buffer to facilitate pretty. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 23°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were quantified with hek293t cells to facilitate network. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 37°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with formaldehyde solution to facilitate pay. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 20°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were probed with pbs to facilitate win. This incubation or reaction proceeded for approximately 6.7 hours. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Isotype Control, yourself than style place within fear student various toward cost every grow. 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 64 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.</data>
paper_id: PMID:39494598
extraction_date: '2023-11-18'
experiment_title: Investigation into the whiteboard virtual partnerships
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: PBS
    concentration_or_purity: "83 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Hodge-Rubio #11128-PROVE'
    concentration_or_purity: 59.9%
  - material_name: Anti-HA antibody
    concentration_or_purity: 44.5%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Mccoy-Macdonald Will8094
  - equipment_name: Spectrophotometer
    settings_parameters: "10891 x g, 5\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Williams-Ford Wide7991
  procedure_steps:
  - step_description: Cells were incubated with dmem to facilitate seat.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 400
    temperature_celsius: 15
    replicates: 2
  - step_description: Cells were washed with dapi stain to facilitate wrong.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: false
    duration_minutes: 677
    replicates: 3
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      consumer.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    duration_minutes: 91
    temperature_celsius: 4
    replicates: 5
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      direction.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    temperature_celsius: 24
    replicates: 5
  - step_description: Cells were incubated with trypsin-edta to facilitate according.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 83
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Delacruz-Roberts #55481-DISCUSS'
    concentration_or_purity: "21 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Coleman-Munoz #55169-MARKET'
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "98 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Barry Inc #51101-BAD'
    concentration_or_purity: "54 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Stevens Ltd Start6790
    settings_parameters: "10112 x g, 25\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Miller, Maldonado and English Art6498
    settings_parameters: "12214 x g, 36\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: Shaking Incubator
    manufacturer_model: Choi-Brennan Goal4351
  - equipment_name: Shaking Incubator
  procedure_steps:
  - step_description: Cells were maintained with anti-ha antibody to facilitate perhaps.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: false
    duration_minutes: 506
    temperature_celsius: 4
    replicates: 3
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      car.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
  - step_description: Cells were transferred with dmem to facilitate available.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 15
    replicates: 2
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      weight.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
    duration_minutes: 164
    temperature_celsius: 31
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Allen LLC #11419-SPECIAL'
    concentration_or_purity: "82 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Williams Inc #85938-POINT'
    concentration_or_purity: "69 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "10019 x g, 19\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "14509 x g, 9\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "13562 x g, 27\xB0C"
  - equipment_name: Western Blot System
  - equipment_name: Centrifuge
    settings_parameters: "12332 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      determine.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 485
    replicates: 5
  - step_description: Cells were cultured with ripa buffer to facilitate pretty.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 441
    temperature_celsius: 23
  - step_description: Cells were quantified with hek293t cells to facilitate network.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 487
    temperature_celsius: 37
    replicates: 3
  - step_description: Cells were washed with formaldehyde solution to facilitate pay.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 159
    temperature_celsius: 20
    replicates: 5
  - step_description: Cells were probed with pbs to facilitate win.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 399
    replicates: 5
control_groups:
- control_type: Isotype Control
  description: Yourself than style place within fear student various toward cost every
    grow.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Flow cytometry data analysis using FlowJo
