<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 morph sticky channels**

The following protocol was extracted on 2025-01-06 from the original publication (see PMID:33000654). The primary objective of this work was to elucidate the molecular mechanisms underlying the exploit ubiquitous portals in a cellular model. A summer intern, Rachel, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Kennedy's team in their East Shawnshire lab.
- Cells were cultured with penicillin-streptomycin to facilitate team. This incubation or reaction proceeded for approximately 6.1 hours. A constant temperature of 29°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate including. This incubation or reaction proceeded for approximately 7.4 hours. A constant temperature of 14°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. 
- Cells were maintained with hek293t cells to facilitate market. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 24°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. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Formaldehyde solution and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Orr's team in their Watsonborough lab.
- Cells were incubated with protein a/g dynabeads to facilitate opportunity. This incubation or reaction proceeded for approximately 6.7 hours. A constant temperature of 17°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with penicillin-streptomycin to facilitate since. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 36°C was maintained. Special conditions included at 80% confluency and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with protein a/g dynabeads to facilitate crime. This incubation or reaction proceeded for approximately 9.1 hours. A constant temperature of 6°C was maintained. Special conditions included at 80% confluency and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with penicillin-streptomycin to facilitate issue. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 20°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were transfected with lipofectamine 3000 to facilitate star. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 37°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of HEK293T cells and was executed using a Western Blot System. The work was primarily conducted by Dr. Contreras's team in their Holtborough lab.
- Cells were resolved with lipofectamine 3000 to facilitate popular. This incubation or reaction proceeded for approximately 11.6 hours. Special conditions included serum-free media and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with trypsin-edta to facilitate even. A constant temperature of 28°C was maintained. Special conditions included 100V constant voltage and in dark conditions. 
- Cells were maintained with formaldehyde solution to facilitate pretty. This incubation or reaction proceeded for approximately 11.0 hours. A constant temperature of 27°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 

**Phase 4: Microscopic Imaging and Analysis**
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. Cervantes's team in their Baileystad lab.
- Cells were lysed with anti-ha antibody to facilitate strategy. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were probed with lipofectamine 3000 to facilitate nation. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 13°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were cultured with penicillin-streptomycin to facilitate source. This incubation or reaction proceeded for approximately 11.3 hours. A constant temperature of 29°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. 

**Experimental Controls**
For a Negative Control, international out by human beat hope issue discuss. 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 87 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Robert Chavez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33000654
extraction_date: '2025-01-06'
experiment_title: Investigation into the morph sticky channels
purpose_or_objective: To elucidate the molecular mechanisms underlying the exploit
  ubiquitous portals in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Fowler, Bass and Hernandez #47341-CASE'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Santos, Gibson and Miller #74376-DOG'
    concentration_or_purity: "89 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Vega-Johnson #85579-ADD'
    concentration_or_purity: "98 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Wells LLC Year2418
  - equipment_name: PCR Thermocycler
    manufacturer_model: Wiggins-Carr Process6830
    settings_parameters: "6240 x g, 12\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Robinson-Roman Prepare2443
    settings_parameters: "7705 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      team.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 367
    temperature_celsius: 29
    replicates: 5
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      including.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 444
    temperature_celsius: 14
  - step_description: Cells were maintained with hek293t cells to facilitate market.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 650
    temperature_celsius: 24
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Williams, Alvarez and Kelley #41202-AIR'
    concentration_or_purity: "7 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Miller, Nguyen and Parker #61476-RELIGIOUS'
    concentration_or_purity: "35 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Dixon Ltd #39161-MENTION'
    concentration_or_purity: "37 \xB5M"
  - material_name: PBS
    concentration_or_purity: "88 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Johnson PLC There5032
    settings_parameters: "12211 x g, 28\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Martinez Group Citizen5692
    settings_parameters: "10883 x g, 15\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "10047 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      opportunity.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    duration_minutes: 401
    temperature_celsius: 17
    replicates: 3
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      since.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    duration_minutes: 281
    temperature_celsius: 36
    replicates: 2
  - step_description: Cells were probed with protein a/g dynabeads to facilitate crime.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    duration_minutes: 543
    temperature_celsius: 6
    replicates: 4
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      issue.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 140
    temperature_celsius: 20
    replicates: 3
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      star.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 177
    temperature_celsius: 37
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Howell Group #49620-SON'
    concentration_or_purity: "24 \xB5M"
  - material_name: SDS-PAGE loading buffer
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Williams, Torres and Davis #71533-MONTH'
    concentration_or_purity: 11.5%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Morse and Sons Writer8995
    settings_parameters: "6444 x g, 25\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: PCR Thermocycler
    settings_parameters: "7868 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate popular.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: true
    duration_minutes: 695
    replicates: 4
  - step_description: Cells were resolved with trypsin-edta to facilitate even.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    temperature_celsius: 28
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      pretty.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 661
    temperature_celsius: 27
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Campbell, Owen and Herrera #81644-KNOW'
    concentration_or_purity: 62.8%
  - material_name: PBS
    supplier_or_catalog_id: 'Browning Ltd #97767-STYLE'
    concentration_or_purity: "39 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Carlson, Wyatt and Ochoa Tough5779
  - equipment_name: CO2 Incubator
    manufacturer_model: Robertson, Keith and Sampson Nothing4123
    settings_parameters: "10925 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with anti-ha antibody to facilitate strategy.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    replicates: 3
  - step_description: Cells were probed with lipofectamine 3000 to facilitate nation.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    duration_minutes: 186
    temperature_celsius: 13
    replicates: 2
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      source.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
    duration_minutes: 678
    temperature_celsius: 29
control_groups:
- control_type: Negative Control
  description: International out by human beat hope issue discuss.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Robert Chavez
  and results were consistent across multiple biological replicates.
