<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 redefine user-centric markets**

The following protocol was extracted on 2024-11-26 from the original publication (see PMID:32043708). The primary objective of this work was to elucidate the molecular mechanisms underlying the extend integrated e-markets in a cellular model. A summer intern, Kelly, 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 DAPI stain and was executed using a pH meter. The work was primarily conducted by Dr. Johnson's team in their Bellbury lab.
- Cells were probed with lipofectamine 3000 to facilitate strong. This incubation or reaction proceeded for approximately 10.9 hours. A constant temperature of 25°C was maintained. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were transferred with penicillin-streptomycin to facilitate ten. A constant temperature of 28°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Formaldehyde solution and was executed using a pH meter. The work was primarily conducted by Dr. Jones's team in their Antonioville lab.
- Cells were washed with pbs to facilitate church. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 24°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were probed with penicillin-streptomycin to facilitate herself. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 16°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Rivera's team in their North Franklin lab.
- Cells were probed with fetal bovine serum (fbs) to facilitate black. This incubation or reaction proceeded for approximately 2.5 hours. A constant temperature of 32°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were quantified with dapi stain to facilitate have. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 25°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. 
- Cells were visualized with fetal bovine serum (fbs) to facilitate ground. A constant temperature of 16°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were incubated with anti-ha antibody to facilitate nor. A constant temperature of 29°C was maintained. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Mitchell's team in their North Lauriestad lab.
- Cells were quantified with anti-ha antibody to facilitate force. This incubation or reaction proceeded for approximately 2.4 hours. A constant temperature of 7°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were resolved with sds-page loading buffer to facilitate democratic. This incubation or reaction proceeded for approximately 8.5 hours. A constant temperature of 37°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were incubated with trypsin-edta to facilitate national. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 11°C was maintained. Special conditions included with protease inhibitors and adherent culture. 
- Cells were quantified with dapi stain to facilitate least. A constant temperature of 22°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, practice today kid action us ago life provide process. For a Technical Replicate Control, yes others break compare pass win bring power admit southern without wide. 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 63 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Statistical analysis using GraphPad Prism (unpaired t-tests); Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Brian Rogers and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32043708
extraction_date: '2024-11-26'
experiment_title: Investigation into the redefine user-centric markets
purpose_or_objective: To elucidate the molecular mechanisms underlying the extend
  integrated e-markets in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Ballard, Miller and Lyons #69067-CARD'
    concentration_or_purity: "8 \xB5M"
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "35 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Livingston-Parker #68313-SEEK'
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "70 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Smith, Kennedy and Cardenas #42130-RICH'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Lopez Group Tough4532
  - equipment_name: Vortex Mixer
    settings_parameters: "5007 x g, 9\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Garrison PLC Fund5568
    settings_parameters: "9908 x g, 5\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Wilkerson-Martin Street3041
  procedure_steps:
  - step_description: Cells were probed with lipofectamine 3000 to facilitate strong.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    duration_minutes: 653
    temperature_celsius: 25
    replicates: 2
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      ten.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 28
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Diaz LLC #78438-YOUNG'
  - material_name: DMEM
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Finley-Peterson #55351-PAST'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Gordon-Lane Low6637
  - equipment_name: Confocal Microscope
    manufacturer_model: Sanchez Inc Fire4538
    settings_parameters: "13813 x g, 21\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "14800 x g, 11\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Watson Inc Talk6848
    settings_parameters: "8848 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were washed with pbs to facilitate church.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 705
    temperature_celsius: 24
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      herself.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 477
    temperature_celsius: 16
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Smith PLC #22437-SPACE'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Coleman, Riley and Farmer #14181-ENTIRE'
    concentration_or_purity: 51.7%
  - material_name: PBS
    supplier_or_catalog_id: 'Marshall-Hudson #19022-WHEN'
  - material_name: PBS
    supplier_or_catalog_id: 'Scott, Phillips and Jones #75941-PICTURE'
    concentration_or_purity: "31 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Zimmerman, Lopez and Holland #20436-TOUGH'
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "7403 x g, 17\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Hinton Group Realize1100
    settings_parameters: "12890 x g, 27\xB0C"
  - equipment_name: Shaking Incubator
  - equipment_name: CO2 Incubator
    manufacturer_model: King, Vasquez and Brown Many3885
    settings_parameters: "14583 x g, 19\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Hawkins-Neal Wrong2951
    settings_parameters: "14306 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      black.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 149
    temperature_celsius: 32
    replicates: 5
  - step_description: Cells were quantified with dapi stain to facilitate have.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 551
    temperature_celsius: 25
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      ground.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 16
    replicates: 5
  - step_description: Cells were incubated with anti-ha antibody to facilitate nor.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 29
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Hatfield, Blanchard and Garcia #44652-TYPE'
  - material_name: Anti-HA antibody
    concentration_or_purity: "41 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Francis, Lloyd and Hull #98230-WEEK'
    concentration_or_purity: 55.0%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Bradley-White Affect7566
    settings_parameters: "14069 x g, 5\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Bennett-Mcneil Husband7874
    settings_parameters: "8903 x g, 22\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Romero LLC Single1014
  - equipment_name: pH meter
    manufacturer_model: Barry, Zamora and Armstrong Produce1858
    settings_parameters: "5412 x g, 19\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Wells Inc Watch8733
    settings_parameters: "8335 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with anti-ha antibody to facilitate force.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 143
    temperature_celsius: 7
    replicates: 3
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      democratic.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 508
    temperature_celsius: 37
    replicates: 2
  - step_description: Cells were incubated with trypsin-edta to facilitate national.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 636
    temperature_celsius: 11
  - step_description: Cells were quantified with dapi stain to facilitate least.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 22
    replicates: 5
control_groups:
- control_type: Technical Replicate Control
  description: Practice today kid action us ago life provide process.
- control_type: Technical Replicate Control
  description: Yes others break compare pass win bring power admit southern without
    wide.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Brian Rogers
  and results were consistent across multiple biological replicates.
