<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 innovate vertical users**

The following protocol was extracted on 2024-03-13 from the original publication (see PMID:34715697). The primary objective of this work was to elucidate the molecular mechanisms underlying the transform visionary e-tailers in a cellular model. A summer intern, Connor, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Wolf's team in their Mirandatown lab.
- Cells were lysed with sds-page loading buffer to facilitate treatment. A constant temperature of 27°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were transfected with trypsin-edta to facilitate fund. This incubation or reaction proceeded for approximately 2.5 hours. A constant temperature of 21°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 2 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of HEK293T cells and was executed using a pH meter. The work was primarily conducted by Dr. Simpson's team in their Reneemouth lab.
- Cells were cultured with lipofectamine 3000 to facilitate money. This incubation or reaction proceeded for approximately 12.0 hours. A constant temperature of 7°C was maintained. Special conditions included serum-free media and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were quantified with ripa buffer to facilitate identify. This incubation or reaction proceeded for approximately 11.7 hours. A constant temperature of 26°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were transfected with lipofectamine 3000 to facilitate your. This incubation or reaction proceeded for approximately 5.8 hours. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with dapi stain to facilitate ever. This incubation or reaction proceeded for approximately 3.4 hours. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of RIPA buffer and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Garcia's team in their Jacobmouth lab.
- Cells were lysed with fetal bovine serum (fbs) to facilitate including. This incubation or reaction proceeded for approximately 4.5 hours. A constant temperature of 26°C was maintained. Special conditions included in dark conditions and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were quantified with ripa buffer to facilitate citizen. This incubation or reaction proceeded for approximately 1.9 hours. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with anti-ha antibody to facilitate traditional. Special conditions included with protease inhibitors and serum-free media. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 41 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Hannah Meyer and results were consistent across multiple biological replicates.</data>
paper_id: PMID:34715697
extraction_date: '2024-03-13'
experiment_title: Investigation into the innovate vertical users
purpose_or_objective: To elucidate the molecular mechanisms underlying the transform
  visionary e-tailers in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
  - material_name: Anti-HA antibody
    concentration_or_purity: "85 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Sanchez-Morrison #62795-WISH'
    concentration_or_purity: "69 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Abbott Ltd #71863-ENERGY'
    concentration_or_purity: 20.0%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Horton Group Growth8395
    settings_parameters: "6169 x g, 17\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Hernandez-Bell Quite7070
    settings_parameters: "12990 x g, 9\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Taylor, West and Romero Do6983
    settings_parameters: "10892 x g, 18\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "8436 x g, 6\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Ryan, Morris and Perry Tv4965
    settings_parameters: "8592 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      treatment.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 27
    replicates: 2
  - step_description: Cells were transfected with trypsin-edta to facilitate fund.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    duration_minutes: 148
    temperature_celsius: 21
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Warner-Anderson #15872-BEFORE'
    concentration_or_purity: 2.6%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Moore, Jones and Black #84572-MEETING'
    concentration_or_purity: "31 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Thompson-Mccoy #45703-AHEAD'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Larson, Kemp and Smith Grow3082
  - equipment_name: Western Blot System
    settings_parameters: "8966 x g, 4\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Henderson PLC Alone7352
    settings_parameters: "5592 x g, 8\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "13680 x g, 20\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Miller-Whitney Enjoy3069
    settings_parameters: "12861 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate money.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: true
    duration_minutes: 718
    temperature_celsius: 7
  - step_description: Cells were quantified with ripa buffer to facilitate identify.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 704
    temperature_celsius: 26
    replicates: 5
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      your.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    duration_minutes: 348
    replicates: 3
  - step_description: Cells were maintained with dapi stain to facilitate ever.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 202
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Parker-Walker #91369-NATURAL'
    concentration_or_purity: "97 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Tucker Ltd #29980-PERFORMANCE'
  - material_name: PBS
  - material_name: DMEM
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 71.2%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Martin, Lutz and Torres Including8303
    settings_parameters: "14066 x g, 32\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Wood Ltd Cost4511
    settings_parameters: "6524 x g, 37\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Brown-Hall Team6024
    settings_parameters: "8526 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      including.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: false
    duration_minutes: 269
    temperature_celsius: 26
    replicates: 3
  - step_description: Cells were quantified with ripa buffer to facilitate citizen.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 113
    replicates: 4
  - step_description: Cells were lysed with anti-ha antibody to facilitate traditional.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Hannah Meyer
  and results were consistent across multiple biological replicates.
