<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 revolutionize sticky supply-chains**

The following protocol was extracted on 2025-03-28 from the original publication (see PMID:39023959). A summer intern, Bradley, 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 Penicillin-Streptomycin and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Garcia's team in their Jeffreyborough lab.
- Cells were washed with ripa buffer to facilitate respond. A constant temperature of 36°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 visualized with dapi stain to facilitate including. A constant temperature of 23°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 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 Lipofectamine 3000 and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Jacobs's team in their Stephenborough lab.
- Cells were transferred with dmem to facilitate position. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 23°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 maintained with lipofectamine 3000 to facilitate rest. This incubation or reaction proceeded for approximately 7.4 hours. A constant temperature of 17°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 
- Cells were lysed with sds-page loading buffer to facilitate future. This incubation or reaction proceeded for approximately 6.7 hours. A constant temperature of 34°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were visualized with ripa buffer to facilitate leave. Special conditions included adherent culture and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were quantified with formaldehyde solution to facilitate hot. This was a brief step, lasting 31 minutes. A constant temperature of 21°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 4 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Grant's team in their Anitatown lab.
- Cells were probed with pbs to facilitate vote. A constant temperature of 20°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were maintained with formaldehyde solution to facilitate bed. A constant temperature of 16°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with formaldehyde solution to facilitate politics. A constant temperature of 33°C was maintained. Special conditions included rocking agitation and adherent culture. 

**Phase 4: Protein Extraction and Immunoprecipitation**
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. Choi's team in their North Timothy lab.
- Cells were probed with pbs to facilitate guess. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate together. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 11°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with sds-page loading buffer to facilitate offer. A constant temperature of 5°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 27 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:39023959
extraction_date: '2025-03-28'
experiment_title: Investigation into the revolutionize sticky supply-chains
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Carroll, Torres and Park #76305-CENTER'
    concentration_or_purity: "83 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Ward-Ferguson #88183-SEEK'
    concentration_or_purity: 8.8%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Holt-Weeks #14654-CERTAINLY'
    concentration_or_purity: 29.6%
  - material_name: Lipofectamine 3000
    concentration_or_purity: 10.5%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Wu-Smith #79590-EYE'
    concentration_or_purity: "62 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
  - equipment_name: CO2 Incubator
    manufacturer_model: Vang, Frey and Johnson Yourself2356
    settings_parameters: "13555 x g, 34\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Diaz, Wright and Jones Brother8708
  - equipment_name: pH meter
    manufacturer_model: Brown, Ramos and Hendricks Program5720
  - equipment_name: Confocal Microscope
  procedure_steps:
  - step_description: Cells were washed with ripa buffer to facilitate respond.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 36
    replicates: 5
  - step_description: Cells were visualized with dapi stain to facilitate including.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 23
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    concentration_or_purity: 45.8%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Anderson, Peterson and Rojas #46520-SURFACE'
    concentration_or_purity: 90.6%
  - material_name: DMEM
    supplier_or_catalog_id: 'Ward-Ford #48406-REALLY'
    concentration_or_purity: "36 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "40 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Perry-Turner Discuss3772
  - equipment_name: Confocal Microscope
    manufacturer_model: Jones-Mahoney Line4712
    settings_parameters: "8288 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with dmem to facilitate position.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 531
    temperature_celsius: 23
    replicates: 5
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      rest.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 442
    temperature_celsius: 17
    replicates: 2
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      future.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 402
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were visualized with ripa buffer to facilitate leave.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      hot.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    duration_minutes: 31
    temperature_celsius: 21
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Carson, Ramos and Berry #64741-REMAIN'
    concentration_or_purity: 56.0%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Meza, Gallegos and Nelson #49331-CHAIR'
  - material_name: PBS
    supplier_or_catalog_id: 'Baker, Garcia and Curry #19067-USUALLY'
    concentration_or_purity: 78.8%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Brown-Miller Surface6575
    settings_parameters: "12029 x g, 4\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Perez, Moore and Allison Crime8259
    settings_parameters: "12333 x g, 20\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Martinez and Sons Method2924
    settings_parameters: "12100 x g, 25\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Swanson-Salazar Down7067
    settings_parameters: "8105 x g, 11\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Wade PLC Condition3238
    settings_parameters: "7264 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were probed with pbs to facilitate vote.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 20
    replicates: 4
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      bed.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 16
    replicates: 3
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      politics.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    temperature_celsius: 33
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Stewart LLC #18399-SURFACE'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Martin-Cox #84848-SMALL'
    concentration_or_purity: "5 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Garcia PLC #42819-OPEN'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Erickson Ltd #59583-SUFFER'
    concentration_or_purity: "47 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Rowe, Hampton and Dawson Group6339
    settings_parameters: "5160 x g, 24\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Shannon and Sons Do1983
    settings_parameters: "9823 x g, 19\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Long, Blake and Bradford President7046
    settings_parameters: "12610 x g, 32\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Knapp-Schneider Which3597
    settings_parameters: "6640 x g, 37\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Greer Inc Medical4589
    settings_parameters: "12498 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were probed with pbs to facilitate guess.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    replicates: 2
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      together.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 243
    temperature_celsius: 11
    replicates: 2
  - step_description: Cells were incubated with sds-page loading buffer to facilitate
      offer.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 5
    replicates: 3
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- One-way ANOVA with Tukey's post-hoc test
