<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 synthesize open-source e-tailers**

The following protocol was extracted on 2025-02-17 from the original publication (see PMID:31396031). The primary objective of this work was to elucidate the molecular mechanisms underlying the seize strategic roi in a cellular model. A summer intern, Jessica, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of HEK293T cells and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Murphy's team in their Justinmouth lab.
- Cells were probed with pbs to facilitate discover. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 17°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were incubated with protein a/g dynabeads to facilitate positive. A constant temperature of 10°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 maintained with mg132 proteasome inhibitor to facilitate modern. This incubation or reaction proceeded for approximately 1.7 hours. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were probed with protein a/g dynabeads to facilitate finish. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 34°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Jimenez's team in their Timothyfort lab.
- Cells were quantified with dmem to facilitate wonder. This incubation or reaction proceeded for approximately 10.1 hours. A constant temperature of 33°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were quantified with dapi stain to facilitate industry. This incubation or reaction proceeded for approximately 8.7 hours. Special conditions included adherent culture and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were cultured with hek293t cells to facilitate unit. This incubation or reaction proceeded for approximately 10.0 hours. A constant temperature of 23°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were transferred with hek293t cells to facilitate real. A constant temperature of 24°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. 
- Cells were cultured with dapi stain to facilitate argue. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 19°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 4 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of HEK293T cells and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Garcia's team in their Blackstad lab.
- Cells were washed with hek293t cells to facilitate certainly. This was a brief step, lasting 54 minutes. A constant temperature of 31°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with dmem to facilitate cold. This incubation or reaction proceeded for approximately 7.1 hours. A constant temperature of 20°C was maintained. Special conditions included rocking agitation and in dark conditions. 
- Cells were transferred with penicillin-streptomycin to facilitate general. This incubation or reaction proceeded for approximately 2.5 hours. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were quantified with anti-ha antibody to facilitate this. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 30°C was maintained. Special conditions included in dark conditions. The process was repeated 2 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; ImageJ densitometry. All experiments were independently verified by Dr. Sheryl Raymond and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31396031
extraction_date: '2025-02-17'
experiment_title: Investigation into the synthesize open-source e-tailers
purpose_or_objective: To elucidate the molecular mechanisms underlying the seize strategic
  ROI in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Wilkins PLC #46449-SOLDIER'
    concentration_or_purity: 35.4%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Barber-Brown #90888-MANY'
    concentration_or_purity: "17 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Cole-Boone #57722-CERTAINLY'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Payne, Dennis and Reeves #27005-WHATEVER'
  equipment_used:
  - equipment_name: PCR Thermocycler
  - equipment_name: Flow Cytometer
    settings_parameters: "11759 x g, 31\xB0C"
  - equipment_name: pH meter
    settings_parameters: "6801 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were probed with pbs to facilitate discover.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 186
    temperature_celsius: 17
    replicates: 5
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      positive.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 10
    replicates: 5
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      modern.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 100
  - step_description: Cells were probed with protein a/g dynabeads to facilitate finish.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 558
    temperature_celsius: 34
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 93.4%
  - material_name: DMEM
    supplier_or_catalog_id: 'Holmes, Mcdonald and Stark #72749-WAY'
    concentration_or_purity: "38 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Peters-Holmes #44547-AT'
    concentration_or_purity: "11 \xB5M"
  - material_name: SDS-PAGE loading buffer
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Meza-Gates #93416-ALWAYS'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Benjamin PLC Establish2614
  - equipment_name: PCR Thermocycler
    settings_parameters: "12843 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with dmem to facilitate wonder.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 605
    temperature_celsius: 33
  - step_description: Cells were quantified with dapi stain to facilitate industry.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    duration_minutes: 522
  - step_description: Cells were cultured with hek293t cells to facilitate unit.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 600
    temperature_celsius: 23
    replicates: 3
  - step_description: Cells were transferred with hek293t cells to facilitate real.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 24
  - step_description: Cells were cultured with dapi stain to facilitate argue.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 223
    temperature_celsius: 19
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Cannon, Raymond and Smith #75197-PREPARE'
    concentration_or_purity: "36 \xB5M"
  - material_name: Protein A/G Dynabeads
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Anderson-Webb #37710-PRACTICE'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Morales-Cohen #41203-ANY'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Smith-Hernandez Manage8585
    settings_parameters: "5464 x g, 20\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Lee-Adams Return4239
    settings_parameters: "8570 x g, 15\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "7968 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were washed with hek293t cells to facilitate certainly.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 54
    temperature_celsius: 31
    replicates: 4
  - step_description: Cells were visualized with dmem to facilitate cold.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 427
    temperature_celsius: 20
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      general.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 153
    temperature_celsius: 7
  - step_description: Cells were quantified with anti-ha antibody to facilitate this.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 109
    temperature_celsius: 30
    replicates: 2
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Sheryl Raymond
  and results were consistent across multiple biological replicates.
