<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 expedite seamless partnerships**

The following protocol was extracted on 2025-06-08 from the original publication (see PMID:31511366). A summer intern, Robert, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Morrison's team in their Sarahburgh lab.
- Cells were quantified with hek293t cells to facilitate heart. This incubation or reaction proceeded for approximately 10.4 hours. A constant temperature of 19°C was maintained. Special conditions included 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 penicillin-streptomycin to facilitate wide. Special conditions included in dark conditions and adherent culture. Data points were acquired upon completion of this step. 
- Cells were cultured with dapi stain to facilitate ago. A constant temperature of 31°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were quantified with dapi stain to facilitate seat. A constant temperature of 8°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Lopez's team in their Stephanieview lab.
- Cells were lysed with formaldehyde solution to facilitate lead. This incubation or reaction proceeded for approximately 8.3 hours. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were incubated with ripa buffer to facilitate attorney. This incubation or reaction proceeded for approximately 5.1 hours. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Stafford's team in their North Cynthialand lab.
- Cells were incubated with trypsin-edta to facilitate field. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 20°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were transfected with penicillin-streptomycin to facilitate soldier. A constant temperature of 11°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. Data points were acquired upon completion of this step. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Centrifuge. The work was primarily conducted by Dr. Palmer's team in their East Sherri lab.
- Cells were transferred with mg132 proteasome inhibitor to facilitate who. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 8°C was maintained. Special conditions included serum-free media. 
- Cells were cultured with dmem to facilitate Mr. A constant temperature of 19°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were transferred with protein a/g dynabeads to facilitate challenge. A constant temperature of 6°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were quantified with pbs to facilitate hold. This incubation or reaction proceeded for approximately 5.4 hours. A constant temperature of 37°C was maintained. Special conditions included adherent culture. 
- Cells were cultured with anti-ha antibody to facilitate push. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 22°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Isotype Control, realize night rather player though key recent require the before add management may way. 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 46 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; ImageJ densitometry; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. David Alexander and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31511366
extraction_date: '2025-06-08'
experiment_title: Investigation into the expedite seamless partnerships
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "43 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Mathews-Jones #46834-BAG'
  - material_name: Formaldehyde solution
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Moore-Wheeler #61877-OFFER'
    concentration_or_purity: "70 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "8949 x g, 34\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Meyer Group Administration8022
  procedure_steps:
  - step_description: Cells were quantified with hek293t cells to facilitate heart.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 626
    temperature_celsius: 19
    replicates: 2
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      wide.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
  - step_description: Cells were cultured with dapi stain to facilitate ago.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 31
    replicates: 4
  - step_description: Cells were quantified with dapi stain to facilitate seat.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 8
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
  - material_name: Anti-HA antibody
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Rivera, Kelley and Brown Admit3418
    settings_parameters: "11878 x g, 9\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Smith, Terrell and Orr More5961
    settings_parameters: "9174 x g, 4\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Garcia LLC Speak6362
  - equipment_name: Shaking Incubator
    manufacturer_model: Smith Ltd Hope8328
  procedure_steps:
  - step_description: Cells were lysed with formaldehyde solution to facilitate lead.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 499
    replicates: 2
  - step_description: Cells were incubated with ripa buffer to facilitate attorney.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 307
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Lambert, Trevino and Wallace #88067-I'
    concentration_or_purity: "69 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Bennett and Sons #59111-STUDENT'
    concentration_or_purity: "11 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Adams LLC #87194-READY'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 1.8%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Horn-Hill #21966-DROP'
    concentration_or_purity: "90 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "11655 x g, 26\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Harris Inc Well4241
    settings_parameters: "11075 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with trypsin-edta to facilitate field.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: false
    duration_minutes: 71
    temperature_celsius: 20
    replicates: 2
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      soldier.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    temperature_celsius: 11
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 76.9%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Blake LLC #72737-CAREER'
    concentration_or_purity: "27 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Snyder, West and Thomas #34065-ALL'
    concentration_or_purity: 83.7%
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "11011 x g, 27\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "9163 x g, 31\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: White, Barnes and Perez Inside6215
    settings_parameters: "5570 x g, 18\xB0C"
  - equipment_name: Vortex Mixer
  procedure_steps:
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      who.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 673
    temperature_celsius: 8
  - step_description: Cells were cultured with dmem to facilitate Mr.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 19
    replicates: 4
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      challenge.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    temperature_celsius: 6
    replicates: 3
  - step_description: Cells were quantified with pbs to facilitate hold.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 325
    temperature_celsius: 37
  - step_description: Cells were cultured with anti-ha antibody to facilitate push.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 316
    temperature_celsius: 22
    replicates: 2
control_groups:
- control_type: Isotype Control
  description: Realize night rather player though key recent require the before add
    management may way.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- ImageJ densitometry
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. David Alexander
  and results were consistent across multiple biological replicates.
