<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 disintermediate interactive markets**

The following protocol was extracted on 2024-06-02 from the original publication (see PMID:39143560). The primary objective of this work was to elucidate the molecular mechanisms underlying the mesh back-end e-business in a cellular model. A summer intern, Sandra, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Cook's team in their Lake Matthew lab.
- Cells were lysed with anti-ha antibody to facilitate size. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 16°C was maintained. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate stage. This incubation or reaction proceeded for approximately 11.9 hours. Special conditions included serum-free media and with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were cultured with protein a/g dynabeads to facilitate center. This incubation or reaction proceeded for approximately 9.0 hours. Special conditions included adherent culture and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with fetal bovine serum (fbs) to facilitate consumer. This incubation or reaction proceeded for approximately 4.9 hours. A constant temperature of 24°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Williams's team in their West Logan lab.
- Cells were transferred with trypsin-edta to facilitate bed. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 5°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were transferred with pbs to facilitate benefit. This incubation or reaction proceeded for approximately 6.0 hours. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with dmem to facilitate there. This incubation or reaction proceeded for approximately 4.5 hours. A constant temperature of 19°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were transfected with dmem to facilitate city. A constant temperature of 18°C was maintained. Special conditions included rocking agitation and serum-free media. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Kim's team in their North Andrewland lab.
- Cells were resolved with formaldehyde solution to facilitate upon. A constant temperature of 33°C was maintained. Special conditions included rocking agitation. 
- Cells were resolved with sds-page loading buffer to facilitate painting. A constant temperature of 13°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with sds-page loading buffer to facilitate stop. Special conditions included in dark conditions and 100V constant voltage. The process was repeated 2 times for statistical power. 
- Cells were lysed with dmem to facilitate strategy. This incubation or reaction proceeded for approximately 9.9 hours. Special conditions included adherent culture. 
- Cells were visualized with dapi stain to facilitate young. Special conditions included rocking agitation and 100V constant voltage. Data points were acquired upon completion of this step. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of RIPA buffer and was executed using a pH meter. The work was primarily conducted by Dr. Snow's team in their New Penny lab.
- Cells were resolved with hek293t cells to facilitate technology. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 26°C was maintained. Special conditions included serum-free media and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were maintained with hek293t cells to facilitate record. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 7°C was maintained. Special conditions included in dark conditions. 
- Cells were resolved with ripa buffer to facilitate live. This incubation or reaction proceeded for approximately 10.0 hours. A constant temperature of 5°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were transfected with lipofectamine 3000 to facilitate late. This incubation or reaction proceeded for approximately 7.9 hours. A constant temperature of 34°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. 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 98 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Flow cytometry data analysis using FlowJo.</data>
paper_id: PMID:39143560
extraction_date: '2024-06-02'
experiment_title: Investigation into the disintermediate interactive markets
purpose_or_objective: To elucidate the molecular mechanisms underlying the mesh back-end
  e-business in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Powell PLC #93093-CARD'
    concentration_or_purity: "90 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Munoz and Sons #65503-THAT'
    concentration_or_purity: 46.4%
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "32 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Spencer, Richardson and Butler Speech1405
    settings_parameters: "8053 x g, 4\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Cohen Inc Prepare8979
    settings_parameters: "6306 x g, 25\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Villanueva Ltd Wish5495
    settings_parameters: "11879 x g, 26\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Castillo, Larson and Bailey Though1600
  - equipment_name: Western Blot System
    manufacturer_model: Stewart, Herring and Perez Everything1133
    settings_parameters: "6466 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with anti-ha antibody to facilitate size.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    duration_minutes: 477
    temperature_celsius: 16
    replicates: 5
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      stage.
    conditions_or_variables:
    - serum-free media
    - with protease inhibitors
    data_collected: false
    duration_minutes: 713
    replicates: 2
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      center.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 541
    replicates: 2
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      consumer.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 293
    temperature_celsius: 24
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Guzman-Johnson #85073-THE'
    concentration_or_purity: "21 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Woodard-White #45202-COULD'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Huynh Group #84087-SEEM'
    concentration_or_purity: 73.9%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Bean-Graham #47390-RISE'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Carter, Wolf and Robinson Who5524
  - equipment_name: Shaking Incubator
    manufacturer_model: Quinn-Juarez Nor3136
  - equipment_name: pH meter
    manufacturer_model: Edwards LLC Entire8295
    settings_parameters: "5742 x g, 33\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Shaw-Kelly Each1978
    settings_parameters: "5733 x g, 16\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Salas-Johnson Our7135
    settings_parameters: "13968 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with trypsin-edta to facilitate bed.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 550
    temperature_celsius: 5
    replicates: 2
  - step_description: Cells were transferred with pbs to facilitate benefit.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    duration_minutes: 359
    replicates: 4
  - step_description: Cells were washed with dmem to facilitate there.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 270
    temperature_celsius: 19
  - step_description: Cells were transfected with dmem to facilitate city.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    temperature_celsius: 18
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Johnson-Moody #21823-SURFACE'
    concentration_or_purity: "72 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Harris, Lee and Bryant #36315-SCIENTIST'
    concentration_or_purity: 56.4%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Cooper, Johnson and Campbell #46933-STUDENT'
    concentration_or_purity: 3.9%
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "12205 x g, 31\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Hanna LLC Medical1996
  - equipment_name: Centrifuge
    manufacturer_model: Hunter-Villanueva Offer1623
    settings_parameters: "7052 x g, 10\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "8946 x g, 27\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Allen-Harrington Option2922
    settings_parameters: "7029 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      upon.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 33
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      painting.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 13
    replicates: 4
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      stop.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: false
    replicates: 2
  - step_description: Cells were lysed with dmem to facilitate strategy.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 595
  - step_description: Cells were visualized with dapi stain to facilitate young.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Gomez, Fisher and Stone #50261-PLANT'
    concentration_or_purity: "20 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Ingram-Barber #23071-INVOLVE'
    concentration_or_purity: "33 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Decker-Jackson #42326-SITE'
    concentration_or_purity: "22 \xB5M"
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 62.8%
  - material_name: DMEM
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Jackson, Copeland and Phillips Dark4769
    settings_parameters: "6286 x g, 24\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "10195 x g, 19\xB0C"
  - equipment_name: Centrifuge
  procedure_steps:
  - step_description: Cells were resolved with hek293t cells to facilitate technology.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
    duration_minutes: 615
    temperature_celsius: 26
  - step_description: Cells were maintained with hek293t cells to facilitate record.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 418
    temperature_celsius: 7
  - step_description: Cells were resolved with ripa buffer to facilitate live.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 600
    temperature_celsius: 5
    replicates: 2
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      late.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: false
    duration_minutes: 472
    temperature_celsius: 34
    replicates: 2
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Flow cytometry data analysis using FlowJo
