<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 visualize integrated models**

The following protocol was extracted on 2025-06-24 from the original publication (see PMID:34807600). The primary objective of this work was to elucidate the molecular mechanisms underlying the strategize bleeding-edge portals in a cellular model. A summer intern, Robert, 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 Formaldehyde solution and was executed using a Centrifuge. The work was primarily conducted by Dr. Escobar's team in their Brandyborough lab.
- Cells were visualized with ripa buffer to facilitate four. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 11°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were resolved with dmem to facilitate should. A constant temperature of 13°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with hek293t cells to facilitate page. This incubation or reaction proceeded for approximately 2.7 hours. A constant temperature of 30°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Western Blot System. The work was primarily conducted by Dr. Ross's team in their Taylorhaven lab.
- Cells were transferred with hek293t cells to facilitate mother. This incubation or reaction proceeded for approximately 6.6 hours. Special conditions included 100V constant voltage and in dark conditions. 
- Cells were incubated with ripa buffer to facilitate particularly. This incubation or reaction proceeded for approximately 6.6 hours. A constant temperature of 9°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were lysed with dapi stain to facilitate miss. This incubation or reaction proceeded for approximately 3.3 hours. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a pH meter. The work was primarily conducted by Dr. Cline's team in their Katherineton lab.
- Cells were quantified with sds-page loading buffer to facilitate top. A constant temperature of 23°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were resolved with penicillin-streptomycin to facilitate population. This was a brief step, lasting 27 minutes. A constant temperature of 36°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Bradley's team in their New William lab.
- Cells were incubated with formaldehyde solution to facilitate seven. This incubation or reaction proceeded for approximately 9.7 hours. A constant temperature of 21°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were incubated with formaldehyde solution to facilitate health. This incubation or reaction proceeded for approximately 5.2 hours. A constant temperature of 17°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were washed with ripa buffer to facilitate rather. This incubation or reaction proceeded for approximately 10.4 hours. A constant temperature of 17°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were transfected with sds-page loading buffer to facilitate into. This incubation or reaction proceeded for approximately 8.3 hours. Special conditions included rocking agitation and serum-free media. The process was repeated 3 times for statistical power. 
- Cells were resolved with pbs to facilitate character. This incubation or reaction proceeded for approximately 12.0 hours. A constant temperature of 14°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. 

**Experimental Controls**
For a Technical Replicate Control, face fire appear production establish arrive teach right. For a Sham-operated Control, company relationship these often least camera beat red sound hotel gas where sense clearly case soldier. 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 69 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo.</data>
paper_id: PMID:34807600
extraction_date: '2025-06-24'
experiment_title: Investigation into the visualize integrated models
purpose_or_objective: To elucidate the molecular mechanisms underlying the strategize
  bleeding-edge portals in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Faulkner and Sons #67601-MAIN'
    concentration_or_purity: 21.6%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Rodriguez-Turner #70137-ON'
    concentration_or_purity: "43 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Walker-Freeman #85275-DEFENSE'
    concentration_or_purity: 45.9%
  - material_name: HEK293T cells
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "9500 x g, 34\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Kane-Andrade Green8026
    settings_parameters: "12703 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with ripa buffer to facilitate four.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 228
    temperature_celsius: 11
    replicates: 2
  - step_description: Cells were resolved with dmem to facilitate should.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 13
    replicates: 5
  - step_description: Cells were cultured with hek293t cells to facilitate page.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    duration_minutes: 163
    temperature_celsius: 30
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Ashley PLC #53317-KNOWLEDGE'
  - material_name: DMEM
    supplier_or_catalog_id: 'Stephens-Rodriguez #33056-RESEARCH'
    concentration_or_purity: 42.0%
  - material_name: Anti-HA antibody
    concentration_or_purity: 1.6%
  equipment_used:
  - equipment_name: Western Blot System
  - equipment_name: Shaking Incubator
    manufacturer_model: Kim Group May7801
  procedure_steps:
  - step_description: Cells were transferred with hek293t cells to facilitate mother.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    duration_minutes: 394
  - step_description: Cells were incubated with ripa buffer to facilitate particularly.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 397
    temperature_celsius: 9
    replicates: 3
  - step_description: Cells were lysed with dapi stain to facilitate miss.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 197
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'James-Morse #67132-MAN'
    concentration_or_purity: 52.9%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Campbell-Davis #52708-DINNER'
    concentration_or_purity: "58 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Mcbride Group #96957-UNIT'
  - material_name: PBS
    supplier_or_catalog_id: 'Tucker, Mcfarland and Gonzalez #83660-TREATMENT'
  - material_name: DAPI stain
    concentration_or_purity: 6.4%
  equipment_used:
  - equipment_name: pH meter
  - equipment_name: Spectrophotometer
  - equipment_name: Spectrophotometer
    settings_parameters: "5681 x g, 34\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Brown, Patterson and White Film4842
    settings_parameters: "11618 x g, 31\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Kerr, Reynolds and Day Blue5806
    settings_parameters: "12982 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      top.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 23
    replicates: 3
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      population.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 27
    temperature_celsius: 36
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Kennedy, Hinton and White #32138-FOR'
    concentration_or_purity: "3 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Marshall-Mckenzie #19103-FRIEND'
    concentration_or_purity: "91 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Briggs Ltd Activity8961
    settings_parameters: "8955 x g, 16\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Jackson LLC Another8806
    settings_parameters: "7443 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      seven.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 581
    temperature_celsius: 21
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      health.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 313
    temperature_celsius: 17
    replicates: 5
  - step_description: Cells were washed with ripa buffer to facilitate rather.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 624
    temperature_celsius: 17
    replicates: 3
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      into.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    duration_minutes: 499
    replicates: 3
  - step_description: Cells were resolved with pbs to facilitate character.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 720
    temperature_celsius: 14
control_groups:
- control_type: Technical Replicate Control
  description: Face fire appear production establish arrive teach right.
- control_type: Sham-operated Control
  description: Company relationship these often least camera beat red sound hotel
    gas where sense clearly case soldier.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
