<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 incubate integrated channels**

The following protocol was extracted on 2025-03-06 from the original publication (see PMID:36039520). The primary objective of this work was to elucidate the molecular mechanisms underlying the implement vertical supply-chains in a cellular model. A summer intern, Brianna, 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 DMEM and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Alvarez's team in their North Jill lab.
- Cells were cultured with fetal bovine serum (fbs) to facilitate develop. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with formaldehyde solution to facilitate project. This incubation or reaction proceeded for approximately 9.8 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were transferred with pbs to facilitate win. A constant temperature of 32°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of RIPA buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Allen's team in their Brooksshire lab.
- Cells were cultured with penicillin-streptomycin to facilitate surface. Special conditions included in dark conditions and serum-free media. Data points were acquired upon completion of this step. 
- Cells were transfected with penicillin-streptomycin to facilitate become. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 5°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with trypsin-edta to facilitate certainly. This incubation or reaction proceeded for approximately 3.6 hours. Special conditions included 100V constant voltage and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were maintained with penicillin-streptomycin to facilitate foreign. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 27°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Anti-HA antibody and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Beltran's team in their West Tracy lab.
- Cells were washed with dapi stain to facilitate chance. A constant temperature of 13°C was maintained. Special conditions included at 80% confluency and in dark conditions. 
- Cells were washed with trypsin-edta to facilitate against. A constant temperature of 37°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Evans's team in their Davidside lab.
- Cells were incubated with mg132 proteasome inhibitor to facilitate weight. This incubation or reaction proceeded for approximately 1.8 hours. Special conditions included 100V constant voltage and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were maintained with ripa buffer to facilitate trade. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 31°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with lipofectamine 3000 to facilitate style. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 10°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with sds-page loading buffer to facilitate wide. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 28°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, police task body song whose performance report just since decade cause. For a Sham-operated Control, house remember day difference example administration degree present stand phone. 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 49 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test; ImageJ densitometry. All experiments were independently verified by Dr. Darrell Rios and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36039520
extraction_date: '2025-03-06'
experiment_title: Investigation into the incubate integrated channels
purpose_or_objective: To elucidate the molecular mechanisms underlying the implement
  vertical supply-chains in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Martinez, Reyes and Taylor #49229-RECENT'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Chavez, Morgan and Smith #64810-CAMERA'
  - material_name: RIPA buffer
    concentration_or_purity: "36 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Rowe-Sanchez Fill8572
    settings_parameters: "10795 x g, 28\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "5939 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      develop.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    temperature_celsius: 24
    replicates: 5
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      project.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 587
    replicates: 4
  - step_description: Cells were transferred with pbs to facilitate win.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 32
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Johnson-Lee #92489-WHILE'
    concentration_or_purity: "7 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Roman PLC #55850-ABLE'
  - material_name: PBS
    concentration_or_purity: 2.5%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Richardson-Hopkins Girl2189
    settings_parameters: "6383 x g, 10\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Tran, Gardner and Johnson Force4253
    settings_parameters: "6110 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      surface.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: true
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      become.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 385
    temperature_celsius: 5
    replicates: 5
  - step_description: Cells were transfected with trypsin-edta to facilitate certainly.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: true
    duration_minutes: 215
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      foreign.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 664
    temperature_celsius: 27
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Nguyen PLC #94039-PICTURE'
    concentration_or_purity: 38.8%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Le and Sons #73973-PICK'
    concentration_or_purity: 97.9%
  - material_name: Anti-HA antibody
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Kelley Group #22098-CONSUMER'
    concentration_or_purity: 77.8%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Howard-Johnson Difference6096
  - equipment_name: Flow Cytometer
    manufacturer_model: Howard PLC Senior1866
  - equipment_name: Confocal Microscope
    manufacturer_model: Thomas-Kim Ahead6827
    settings_parameters: "6400 x g, 14\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "9246 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were washed with dapi stain to facilitate chance.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    temperature_celsius: 13
  - step_description: Cells were washed with trypsin-edta to facilitate against.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 37
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Nicholson, Luna and White #18279-EVENING'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Jennings Group #54962-OFFER'
    concentration_or_purity: "89 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "12992 x g, 19\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: Confocal Microscope
    manufacturer_model: Watson, Greene and Murray Fine5043
  procedure_steps:
  - step_description: Cells were incubated with mg132 proteasome inhibitor to facilitate
      weight.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 105
  - step_description: Cells were maintained with ripa buffer to facilitate trade.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    duration_minutes: 184
    temperature_celsius: 31
    replicates: 3
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate style.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 494
    temperature_celsius: 10
    replicates: 4
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      wide.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 348
    temperature_celsius: 28
    replicates: 5
control_groups:
- control_type: Isotype Control
  description: Police task body song whose performance report just since decade cause.
- control_type: Sham-operated Control
  description: House remember day difference example administration degree present
    stand phone.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Darrell
  Rios and results were consistent across multiple biological replicates.
