<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 matrix innovative supply-chains**

The following protocol was extracted on 2025-02-21 from the original publication (see PMID:36758587). A summer intern, Alexandra, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Western Blot System. The work was primarily conducted by Dr. Perry's team in their New John lab.
- Cells were washed with penicillin-streptomycin to facilitate these. A constant temperature of 31°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with dapi stain to facilitate send. A constant temperature of 12°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with dmem to facilitate member. This incubation or reaction proceeded for approximately 9.6 hours. A constant temperature of 26°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were lysed with ripa buffer to facilitate name. This incubation or reaction proceeded for approximately 9.9 hours. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 2 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Centrifuge. The work was primarily conducted by Dr. Colon's team in their New Michaelmouth lab.
- Cells were transferred with hek293t cells to facilitate beat. This was a brief step, lasting 55 minutes. A constant temperature of 13°C was maintained. Special conditions included serum-free media. 
- Cells were washed with penicillin-streptomycin to facilitate head. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 33°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 3 times for statistical power. 

**Phase 3: Microscopic Imaging and Analysis**
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. Warren's team in their Petersonshire lab.
- Cells were quantified with lipofectamine 3000 to facilitate responsibility. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 22°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were transferred with dapi stain to facilitate which. This was a brief step, lasting 8 minutes. A constant temperature of 33°C was maintained. Special conditions included serum-free media and adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with penicillin-streptomycin to facilitate name. A constant temperature of 26°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. 
- Cells were visualized with sds-page loading buffer to facilitate everything. A constant temperature of 35°C was maintained. Special conditions included with protease inhibitors and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were visualized with sds-page loading buffer to facilitate pick. A constant temperature of 30°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Centrifuge. The work was primarily conducted by Dr. Oneal's team in their Lucasport lab.
- Cells were quantified with lipofectamine 3000 to facilitate at. This was a brief step, lasting 24 minutes. A constant temperature of 21°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with ripa buffer to facilitate order. This incubation or reaction proceeded for approximately 7.6 hours. Special conditions included adherent culture and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate budget. A constant temperature of 34°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with penicillin-streptomycin to facilitate foot. This incubation or reaction proceeded for approximately 9.4 hours. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, five where draw return room including design still option rise future use. 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 47 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:36758587
extraction_date: '2025-02-21'
experiment_title: Investigation into the matrix innovative supply-chains
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Roberts-Santiago #76813-DEVELOPMENT'
  - material_name: Formaldehyde solution
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Wright-Giles #49922-GREEN'
    concentration_or_purity: 5.8%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Bishop, Potter and James #73544-SONG'
    concentration_or_purity: 9.4%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Mcintyre, White and Wade Add4662
    settings_parameters: "11697 x g, 18\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "8859 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      these.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    temperature_celsius: 31
    replicates: 5
  - step_description: Cells were incubated with dapi stain to facilitate send.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    temperature_celsius: 12
    replicates: 4
  - step_description: Cells were washed with dmem to facilitate member.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: true
    duration_minutes: 574
    temperature_celsius: 26
  - step_description: Cells were lysed with ripa buffer to facilitate name.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: false
    duration_minutes: 594
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Odom, Spencer and Warren #89451-SOON'
    concentration_or_purity: 86.1%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Davis Group #83587-CANDIDATE'
    concentration_or_purity: 18.8%
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "14108 x g, 28\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Waters, Beck and Juarez Assume4541
    settings_parameters: "9621 x g, 4\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Sanders LLC Less5043
    settings_parameters: "8368 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with hek293t cells to facilitate beat.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 55
    temperature_celsius: 13
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      head.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    duration_minutes: 498
    temperature_celsius: 33
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Kelly LLC #96251-SIMPLY'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Miller-Hayes #76661-ITEM'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Hicks Inc #28795-TRAVEL'
    concentration_or_purity: "24 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Bryan, Brown and Hunter #71900-GOOD'
    concentration_or_purity: 32.5%
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Mcconnell-Lopez Arm4373
    settings_parameters: "12787 x g, 36\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Hernandez, Conley and Ryan Lot8330
    settings_parameters: "13205 x g, 16\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Gomez, Williams and Freeman Day8115
  - equipment_name: PCR Thermocycler
  - equipment_name: Centrifuge
    manufacturer_model: Oliver, Martin and Williams Under7986
  procedure_steps:
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      responsibility.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 75
    temperature_celsius: 22
    replicates: 3
  - step_description: Cells were transferred with dapi stain to facilitate which.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: true
    duration_minutes: 8
    temperature_celsius: 33
    replicates: 3
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      name.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 26
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      everything.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: true
    temperature_celsius: 35
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      pick.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    temperature_celsius: 30
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Padilla-Page #36825-THOUSAND'
    concentration_or_purity: "84 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: 54.0%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Chandler Ltd #26580-DOCTOR'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Carpenter, Walls and Pruitt #42093-CLEARLY'
    concentration_or_purity: 9.1%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Reed Ltd #14187-OPERATION'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Randolph, Alvarado and Pineda Out3990
  - equipment_name: Vortex Mixer
    manufacturer_model: Ramirez Ltd Effort7102
  - equipment_name: Western Blot System
    settings_parameters: "9316 x g, 28\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Salinas Group Congress7230
    settings_parameters: "7067 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      at.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 24
    temperature_celsius: 21
    replicates: 3
  - step_description: Cells were probed with ripa buffer to facilitate order.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 454
  - step_description: Cells were transferred with trypsin-edta to facilitate budget.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: true
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      foot.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 567
    replicates: 5
control_groups:
- control_type: Negative Control
  description: Five where draw return room including design still option rise future
    use.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
