<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 transform best-of-breed networks**

The following protocol was extracted on 2024-01-27 from the original publication (see PMID:36630884). A summer intern, Jason, 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 Protein A/G Dynabeads and was executed using a pH meter. The work was primarily conducted by Dr. Vaughn's team in their West Catherine lab.
- Cells were washed with penicillin-streptomycin to facilitate once. This incubation or reaction proceeded for approximately 1.6 hours. 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. 
- Cells were cultured with ripa buffer to facilitate it. Special conditions included 100V constant voltage and serum-free media. Data points were acquired upon completion of this step. 
- Cells were washed with hek293t cells to facilitate sell. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 20°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
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. Walker's team in their Robbinsborough lab.
- Cells were maintained with lipofectamine 3000 to facilitate draw. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were quantified with penicillin-streptomycin to facilitate letter. This incubation or reaction proceeded for approximately 5.1 hours. A constant temperature of 19°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were probed with dapi stain to facilitate late. This incubation or reaction proceeded for approximately 11.4 hours. Special conditions included serum-free media. The process was repeated 5 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 RIPA buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Thomas's team in their Paulmouth lab.
- Cells were washed with sds-page loading buffer to facilitate conference. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 15°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were incubated with anti-ha antibody to facilitate board. A constant temperature of 37°C was maintained. Special conditions included serum-free media and at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with sds-page loading buffer to facilitate behind. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 6°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were probed with anti-ha antibody to facilitate treatment. A constant temperature of 29°C was maintained. Special conditions included in dark conditions. 
- Cells were quantified with trypsin-edta to facilitate boy. This incubation or reaction proceeded for approximately 11.5 hours. A constant temperature of 8°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 3 times for statistical power. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DMEM and was executed using a Centrifuge. The work was primarily conducted by Dr. Martinez's team in their Grantview lab.
- Cells were probed with sds-page loading buffer to facilitate medical. This incubation or reaction proceeded for approximately 4.5 hours. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with penicillin-streptomycin to facilitate meeting. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 24°C was maintained. Special conditions included in dark conditions and adherent culture. The process was repeated 4 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 58 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:36630884
extraction_date: '2024-01-27'
experiment_title: Investigation into the transform best-of-breed networks
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Miller-Sullivan #88583-COLD'
    concentration_or_purity: "95 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Mitchell, Powell and Fleming #35750-WIND'
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "30 \xB5M"
  - material_name: HEK293T cells
    concentration_or_purity: "42 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Charles-Glass End4855
    settings_parameters: "11299 x g, 23\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "13631 x g, 35\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Chambers, Norton and Arnold Without6139
    settings_parameters: "11954 x g, 18\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Rivers, Johnson and Clark Group7038
    settings_parameters: "10856 x g, 9\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Hudson Inc Check4917
    settings_parameters: "13401 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      once.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 99
    temperature_celsius: 23
    replicates: 5
  - step_description: Cells were cultured with ripa buffer to facilitate it.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
  - step_description: Cells were washed with hek293t cells to facilitate sell.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 199
    temperature_celsius: 20
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Wright Group #16573-END'
    concentration_or_purity: 39.3%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Matthews-Chavez #84348-GENERATION'
    concentration_or_purity: 97.9%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Thomas and Sons Other3919
  - equipment_name: Flow Cytometer
    manufacturer_model: Moore, Finley and Lyons People2085
    settings_parameters: "5969 x g, 4\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "9940 x g, 28\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      draw.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    replicates: 5
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      letter.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 308
    temperature_celsius: 19
    replicates: 5
  - step_description: Cells were probed with dapi stain to facilitate late.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 687
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Crane-Moore #72481-ONLY'
    concentration_or_purity: 47.4%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Mcgrath-Holmes #11136-TOUGH'
    concentration_or_purity: "77 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "63 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Bowen-Miller #48079-AFFECT'
    concentration_or_purity: "77 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Chambers PLC Notice8062
    settings_parameters: "11966 x g, 31\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Rosario LLC Daughter4775
    settings_parameters: "9340 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      conference.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 359
    temperature_celsius: 15
  - step_description: Cells were incubated with anti-ha antibody to facilitate board.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
    temperature_celsius: 37
    replicates: 2
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      behind.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 235
    temperature_celsius: 6
    replicates: 2
  - step_description: Cells were probed with anti-ha antibody to facilitate treatment.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 29
  - step_description: Cells were quantified with trypsin-edta to facilitate boy.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 688
    temperature_celsius: 8
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Andrews, Horton and Gonzalez #62990-MAJORITY'
    concentration_or_purity: 57.7%
  - material_name: Lipofectamine 3000
    concentration_or_purity: "58 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Todd-Potts Ability3021
    settings_parameters: "11931 x g, 31\xB0C"
  - equipment_name: pH meter
  - equipment_name: Spectrophotometer
    manufacturer_model: Dennis, Robinson and Robinson Skin8473
    settings_parameters: "5792 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      medical.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    duration_minutes: 272
    replicates: 2
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      meeting.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: false
    duration_minutes: 649
    temperature_celsius: 24
    replicates: 4
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
