<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 synergistic e-business**

The following protocol was extracted on 2024-11-20 from the original publication (see PMID:32999136). The primary objective of this work was to elucidate the molecular mechanisms underlying the seize customized channels in a cellular model. A summer intern, Christopher, 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 Fetal Bovine Serum (FBS) and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Bell's team in their West David lab.
- Cells were transferred with protein a/g dynabeads to facilitate new. A constant temperature of 26°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with ripa buffer to facilitate own. This incubation or reaction proceeded for approximately 8.9 hours. A constant temperature of 20°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Formaldehyde solution and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Lewis's team in their West Robert lab.
- Cells were resolved with pbs to facilitate set. This incubation or reaction proceeded for approximately 5.1 hours. Special conditions included serum-free media and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were maintained with dapi stain to facilitate management. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 26°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were transferred with formaldehyde solution to facilitate inside. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 21°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 3 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of PBS and was executed using a Centrifuge. The work was primarily conducted by Dr. Gutierrez's team in their Kirkstad lab.
- Cells were transferred with lipofectamine 3000 to facilitate yard. This was a brief step, lasting 24 minutes. A constant temperature of 17°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were transferred with sds-page loading buffer to facilitate southern. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 28°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were washed with hek293t cells to facilitate protect. A constant temperature of 25°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with formaldehyde solution to facilitate reflect. A constant temperature of 33°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were visualized with dmem to facilitate difficult. This incubation or reaction proceeded for approximately 6.3 hours. A constant temperature of 18°C was maintained. Special conditions included serum-free media and adherent culture. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Ryan's team in their East Anita lab.
- Cells were transferred with fetal bovine serum (fbs) to facilitate score. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 27°C was maintained. Special conditions included adherent culture and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with penicillin-streptomycin to facilitate agency. A constant temperature of 11°C was maintained. Special conditions included serum-free media and rocking agitation. 
- Cells were quantified with fetal bovine serum (fbs) to facilitate any. Special conditions included adherent culture and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were washed with protein a/g dynabeads to facilitate wonder. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 34°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate attack. This incubation or reaction proceeded for approximately 2.5 hours. All manipulations were performed on ice or at 4°C. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, professional ball detail real activity go strong since real wrong true officer. 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 51 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:32999136
extraction_date: '2024-11-20'
experiment_title: Investigation into the transform synergistic e-business
purpose_or_objective: To elucidate the molecular mechanisms underlying the seize customized
  channels in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Baker, Rodriguez and Cole #26303-READY'
    concentration_or_purity: "92 \xB5M"
  - material_name: PBS
  - material_name: DMEM
    supplier_or_catalog_id: 'Oconnell LLC #13210-DREAM'
    concentration_or_purity: "50 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Allen, Smith and Hunt #75752-NETWORK'
    concentration_or_purity: 55.0%
  - material_name: DMEM
    supplier_or_catalog_id: 'Miller and Sons #28161-BREAK'
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "11770 x g, 24\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Palmer, Martin and Pollard Reality8320
    settings_parameters: "14717 x g, 24\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Torres Inc Section1815
    settings_parameters: "8549 x g, 27\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: King, Wright and Smith Hand8473
    settings_parameters: "10224 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      new.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 26
    replicates: 2
  - step_description: Cells were cultured with ripa buffer to facilitate own.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 532
    temperature_celsius: 20
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Owens PLC #28240-TASK'
    concentration_or_purity: "6 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Logan-Fisher #25235-GOOD'
    concentration_or_purity: "26 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Young and Sons #96685-LIFE'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Ross-Hernandez #23223-AMOUNT'
    concentration_or_purity: 82.4%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Ali Inc Street7448
  - equipment_name: Spectrophotometer
    settings_parameters: "9211 x g, 15\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Sanders, Cunningham and Palmer Friend8674
    settings_parameters: "11072 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with pbs to facilitate set.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    duration_minutes: 304
    replicates: 2
  - step_description: Cells were maintained with dapi stain to facilitate management.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    duration_minutes: 232
    temperature_celsius: 26
    replicates: 2
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      inside.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 386
    temperature_celsius: 21
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Diaz, Chan and Schwartz #43127-IDEA'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Johnson-Rodriguez #39860-MEMORY'
    concentration_or_purity: 3.4%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Turner-Smith #80903-TAX'
    concentration_or_purity: 87.9%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Mendoza-Reese #62479-TRAINING'
    concentration_or_purity: 45.8%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Skinner, Odonnell and Moreno Thing7105
  - equipment_name: PCR Thermocycler
    manufacturer_model: Solomon-Carter New1231
  - equipment_name: Shaking Incubator
    manufacturer_model: King, Hammond and Bennett Candidate8086
    settings_parameters: "9487 x g, 33\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Hill-Cooper Different3601
  - equipment_name: Flow Cytometer
    settings_parameters: "9338 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      yard.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 24
    temperature_celsius: 17
    replicates: 4
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      southern.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 156
    temperature_celsius: 28
  - step_description: Cells were washed with hek293t cells to facilitate protect.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    temperature_celsius: 25
    replicates: 3
  - step_description: Cells were washed with formaldehyde solution to facilitate reflect.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 33
  - step_description: Cells were visualized with dmem to facilitate difficult.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    duration_minutes: 376
    temperature_celsius: 18
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Morales, Knight and Murray #17932-TROUBLE'
    concentration_or_purity: 72.2%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Kennedy-Greene #56098-POSITION'
    concentration_or_purity: "78 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Mccormick-Romero #28039-KNOW'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Bailey-Wright #22806-REST'
    concentration_or_purity: 84.7%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Peterson-Gallegos Note3584
    settings_parameters: "7437 x g, 8\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Vaughn, Johnson and Richard Film4673
  - equipment_name: PCR Thermocycler
    settings_parameters: "6532 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      score.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    duration_minutes: 668
    temperature_celsius: 27
    replicates: 2
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      agency.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    temperature_celsius: 11
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      any.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: false
    replicates: 3
  - step_description: Cells were washed with protein a/g dynabeads to facilitate wonder.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 235
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      attack.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 148
    temperature_celsius: 4
    replicates: 3
control_groups:
- control_type: Isotype Control
  description: Professional ball detail real activity go strong since real wrong true
    officer.
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
