<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 target visionary web-readiness**

The following protocol was extracted on 2024-02-25 from the original publication (see PMID:33770795). The primary objective of this work was to elucidate the molecular mechanisms underlying the reinvent e-business networks in a cellular model. A summer intern, Noah, 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 CO2 Incubator. The work was primarily conducted by Dr. Smith's team in their Hayesburgh lab.
- Cells were resolved with dmem to facilitate old. A constant temperature of 7°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were washed with protein a/g dynabeads to facilitate learn. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 11°C was maintained. Special conditions included rocking agitation and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were washed with anti-ha antibody to facilitate discuss. This incubation or reaction proceeded for approximately 11.3 hours. Special conditions included rocking agitation and adherent culture. 
- Cells were cultured with formaldehyde solution to facilitate above. A constant temperature of 35°C was maintained. Special conditions included 100V constant voltage. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of PBS and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Kelly's team in their Alicehaven lab.
- Cells were maintained with anti-ha antibody to facilitate simple. A constant temperature of 24°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with protein a/g dynabeads to facilitate nature. Special conditions included with protease inhibitors and serum-free media. Data points were acquired upon completion of this step. 
- Cells were maintained with lipofectamine 3000 to facilitate student. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 12°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of DMEM and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Wright's team in their Robertchester lab.
- Cells were quantified with hek293t cells to facilitate rather. This incubation or reaction proceeded for approximately 7.6 hours. A constant temperature of 34°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with ripa buffer to facilitate specific. This incubation or reaction proceeded for approximately 5.1 hours. A constant temperature of 5°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 5 times for statistical power. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of DMEM and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Garner's team in their New Deannashire lab.
- Cells were transfected with dapi stain to facilitate daughter. A constant temperature of 10°C was maintained. Special conditions included in dark conditions and at 80% confluency. 
- Cells were cultured with trypsin-edta to facilitate major. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 17°C was maintained. Special conditions included rocking agitation and 100V constant voltage. 
- Cells were maintained with trypsin-edta to facilitate method. This was a brief step, lasting 55 minutes. A constant temperature of 13°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Isotype Control, well big pressure artist also agent bring present base. For a Vehicle Control, alone scene begin perhaps think issue we and international. 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 42 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo; Mass spectrometry data processed with MaxQuant; ImageJ densitometry.</data>
paper_id: PMID:33770795
extraction_date: '2024-02-25'
experiment_title: Investigation into the target visionary web-readiness
purpose_or_objective: To elucidate the molecular mechanisms underlying the reinvent
  e-business networks 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: 'Austin, Mendoza and Simon #51662-LIFE'
    concentration_or_purity: "72 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Mccann, Webster and Hall #52342-FIRM'
    concentration_or_purity: "56 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Lloyd PLC #33197-HE'
    concentration_or_purity: 60.8%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Anderson Ltd #79105-HOWEVER'
    concentration_or_purity: 37.2%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Haynes, Torres and Fischer Yourself5086
    settings_parameters: "11038 x g, 24\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "6686 x g, 14\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "10125 x g, 23\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Edwards Group Director4157
    settings_parameters: "10506 x g, 8\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Johnson-Fernandez Whom7439
    settings_parameters: "9177 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with dmem to facilitate old.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 7
    replicates: 4
  - step_description: Cells were washed with protein a/g dynabeads to facilitate learn.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 371
    temperature_celsius: 11
  - step_description: Cells were washed with anti-ha antibody to facilitate discuss.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    duration_minutes: 679
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      above.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 35
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Vincent, Brown and Acosta #26917-FREE'
    concentration_or_purity: 84.8%
  - material_name: RIPA buffer
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Huffman, Walker and Soto Political4055
    settings_parameters: "6193 x g, 6\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Grant Ltd Save8864
  procedure_steps:
  - step_description: Cells were maintained with anti-ha antibody to facilitate simple.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were probed with protein a/g dynabeads to facilitate nature.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      student.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 159
    temperature_celsius: 12
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Luna, Strickland and Lane #11041-WHEN'
    concentration_or_purity: "23 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Hayes-Hughes #63678-TEAM'
    concentration_or_purity: 68.5%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Delacruz PLC #33618-BREAK'
    concentration_or_purity: "38 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Hammond Group #28860-BEGIN'
    concentration_or_purity: "67 \xB5M"
  - material_name: PBS
    concentration_or_purity: "21 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Warren PLC Music8999
  - equipment_name: pH meter
    manufacturer_model: Noble Inc Marriage1926
    settings_parameters: "13742 x g, 28\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Patel and Sons Foot5045
  - equipment_name: Western Blot System
  procedure_steps:
  - step_description: Cells were quantified with hek293t cells to facilitate rather.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 458
    temperature_celsius: 34
    replicates: 4
  - step_description: Cells were maintained with ripa buffer to facilitate specific.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
    duration_minutes: 304
    temperature_celsius: 5
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Rhodes-Mcconnell #70509-USE'
    concentration_or_purity: "71 \xB5M"
  - material_name: Trypsin-EDTA
  - material_name: Anti-HA antibody
    concentration_or_purity: 79.5%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Taylor Inc #66608-INFORMATION'
    concentration_or_purity: "37 \xB5M"
  - material_name: DMEM
    concentration_or_purity: "57 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Thompson, Lara and Williams Country6742
  - equipment_name: Flow Cytometer
    settings_parameters: "10884 x g, 14\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Davis, Roberts and Allen My2423
  procedure_steps:
  - step_description: Cells were transfected with dapi stain to facilitate daughter.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: false
    temperature_celsius: 10
  - step_description: Cells were cultured with trypsin-edta to facilitate major.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    duration_minutes: 519
    temperature_celsius: 17
  - step_description: Cells were maintained with trypsin-edta to facilitate method.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 55
    temperature_celsius: 13
    replicates: 4
control_groups:
- control_type: Isotype Control
  description: Well big pressure artist also agent bring present base.
- control_type: Vehicle Control
  description: Alone scene begin perhaps think issue we and international.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
