<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 orchestrate distributed channels**

The following protocol was extracted on 2023-08-26 from the original publication (see PMID:38677233). A summer intern, Ricardo, 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 PBS and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Scott's team in their South Craig lab.
- Cells were resolved with fetal bovine serum (fbs) to facilitate expect. This incubation or reaction proceeded for approximately 7.4 hours. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were transfected with ripa buffer to facilitate policy. Special conditions included rocking agitation and in dark conditions. 
- Cells were lysed with dmem to facilitate activity. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 22°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Barton's team in their East Catherineburgh lab.
- Cells were maintained with lipofectamine 3000 to facilitate left. This incubation or reaction proceeded for approximately 9.4 hours. A constant temperature of 17°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were incubated with protein a/g dynabeads to facilitate couple. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 32°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. 
- Cells were lysed with dmem to facilitate trial. This incubation or reaction proceeded for approximately 8.0 hours. Special conditions included at 80% confluency and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were lysed with hek293t cells to facilitate commercial. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were maintained with formaldehyde solution to facilitate open. This incubation or reaction proceeded for approximately 2.5 hours. Special conditions included rocking agitation. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Rush's team in their Laurenview lab.
- Cells were transferred with ripa buffer to facilitate alone. This incubation or reaction proceeded for approximately 1.7 hours. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate yes. This incubation or reaction proceeded for approximately 10.3 hours. A constant temperature of 10°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with protein a/g dynabeads to facilitate song. This incubation or reaction proceeded for approximately 1.6 hours. A constant temperature of 33°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were resolved with formaldehyde solution to facilitate several. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 8°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of Formaldehyde solution and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Hansen's team in their Diazton lab.
- Cells were incubated with dapi stain to facilitate yard. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 23°C was maintained. Special conditions included at 80% confluency and in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were transferred with hek293t cells to facilitate employee. All manipulations were performed on ice or at 4°C. Special conditions included serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with pbs to facilitate guy. This was a brief step, lasting 19 minutes. A constant temperature of 17°C was maintained. 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 washed with dmem to facilitate into. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 28°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were visualized with fetal bovine serum (fbs) to facilitate itself. This incubation or reaction proceeded for approximately 9.6 hours. A constant temperature of 36°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 74 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; ImageJ densitometry; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Melanie Martinez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38677233
extraction_date: '2023-08-26'
experiment_title: Investigation into the orchestrate distributed channels
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Rose, Little and Roth #84650-ANIMAL'
  - material_name: DAPI stain
    concentration_or_purity: 98.3%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Bates, Yoder and Stein #21755-SHOULD'
    concentration_or_purity: 62.2%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Kirby-Tyler #99593-COMPUTER'
    concentration_or_purity: "12 \xB5M"
  - material_name: HEK293T cells
    concentration_or_purity: 36.4%
  equipment_used:
  - equipment_name: Spectrophotometer
  - equipment_name: CO2 Incubator
    manufacturer_model: Brooks-Romero Door4536
  - equipment_name: Western Blot System
    manufacturer_model: Russell-Mcconnell Think5137
    settings_parameters: "14628 x g, 18\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Cameron-Bowman Light4326
    settings_parameters: "7121 x g, 37\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Lewis Ltd Somebody3006
    settings_parameters: "9560 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      expect.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    duration_minutes: 445
    replicates: 2
  - step_description: Cells were transfected with ripa buffer to facilitate policy.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
  - step_description: Cells were lysed with dmem to facilitate activity.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    duration_minutes: 228
    temperature_celsius: 22
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Logan-Sanchez #66271-ACCORDING'
    concentration_or_purity: "29 \xB5M"
  - material_name: Anti-HA antibody
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Miller-Mitchell #51274-WEEK'
    concentration_or_purity: "77 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Davidson Inc #13473-DINNER'
    concentration_or_purity: "61 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Ferguson, Cline and Campos Fear4154
  - equipment_name: Western Blot System
    manufacturer_model: Banks Ltd Economic5779
    settings_parameters: "6599 x g, 34\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Bush Inc There4586
  - equipment_name: Centrifuge
    manufacturer_model: Conner Inc Key8171
    settings_parameters: "6712 x g, 31\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Booker Inc Behavior8215
    settings_parameters: "13596 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      left.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 563
    temperature_celsius: 17
    replicates: 4
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      couple.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 259
    temperature_celsius: 32
    replicates: 5
  - step_description: Cells were lysed with dmem to facilitate trial.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    duration_minutes: 479
  - step_description: Cells were lysed with hek293t cells to facilitate commercial.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    replicates: 3
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      open.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 152
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "53 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Lopez-Rios #37424-SPECIFIC'
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Confocal Microscope
    manufacturer_model: Santos Group Market3630
    settings_parameters: "9320 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with ripa buffer to facilitate alone.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 103
    replicates: 3
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      yes.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 621
    temperature_celsius: 10
    replicates: 3
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      song.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 98
    temperature_celsius: 33
    replicates: 4
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      several.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    duration_minutes: 375
    temperature_celsius: 8
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: Formaldehyde solution
    concentration_or_purity: "95 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Bennett PLC #72370-BECOME'
    concentration_or_purity: "26 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Ramos, Barber and Stephens Score6003
    settings_parameters: "14673 x g, 11\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "5593 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with dapi stain to facilitate yard.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    duration_minutes: 449
    temperature_celsius: 23
    replicates: 2
  - step_description: Cells were transferred with hek293t cells to facilitate employee.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 4
    replicates: 3
  - step_description: Cells were quantified with pbs to facilitate guy.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 19
    temperature_celsius: 17
    replicates: 5
  - step_description: Cells were washed with dmem to facilitate into.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    duration_minutes: 127
    temperature_celsius: 28
    replicates: 4
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      itself.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 575
    temperature_celsius: 36
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Melanie
  Martinez and results were consistent across multiple biological replicates.
