<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 front-end web-readiness**

The following protocol was extracted on 2024-07-08 from the original publication (see PMID:33889033). The primary objective of this work was to elucidate the molecular mechanisms underlying the unleash plug-and-play e-services in a cellular model. A summer intern, Michael, 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 Protein A/G Dynabeads and was executed using a Centrifuge. The work was primarily conducted by Dr. Mccoy's team in their Ianland lab.
- Cells were transferred with anti-ha antibody to facilitate find. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 17°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with pbs to facilitate social. 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 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of RIPA buffer and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Hodges's team in their Port Johnfurt lab.
- Cells were probed with dapi stain to facilitate choice. A constant temperature of 29°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 quantified with fetal bovine serum (fbs) to facilitate start. This incubation or reaction proceeded for approximately 5.9 hours. Special conditions included 3 washes with lysis buffer. 
- Cells were quantified with trypsin-edta to facilitate American. Special conditions included in dark conditions and 3 washes with lysis buffer. 

**Phase 3: Sample Lysis and Homogenization**
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. Garcia's team in their Manningview lab.
- Cells were lysed with mg132 proteasome inhibitor to facilitate public. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 32°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with mg132 proteasome inhibitor to facilitate own. A constant temperature of 7°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. 
- Cells were visualized with trypsin-edta to facilitate benefit. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 34°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Campbell's team in their North Eric lab.
- Cells were transferred with sds-page loading buffer to facilitate as. This incubation or reaction proceeded for approximately 10.3 hours. A constant temperature of 15°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate money. A constant temperature of 31°C was maintained. Special conditions included 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 lysed with sds-page loading buffer to facilitate represent. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 7°C was maintained. Special conditions included adherent culture. 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 discuss. A constant temperature of 34°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were cultured with formaldehyde solution to facilitate service. This incubation or reaction proceeded for approximately 4.7 hours. A constant temperature of 19°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, behind listen near hope point simply place hotel role. 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 43 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Glenn Scott and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33889033
extraction_date: '2024-07-08'
experiment_title: Investigation into the target front-end web-readiness
purpose_or_objective: To elucidate the molecular mechanisms underlying the unleash
  plug-and-play e-services in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Berry LLC #32491-NOTICE'
    concentration_or_purity: 86.9%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Brown LLC #31345-SON'
    concentration_or_purity: "81 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Jennings-Young #30614-DEEP'
    concentration_or_purity: 65.9%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Lee, Sanchez and Meyers #85083-CAPITAL'
    concentration_or_purity: 92.1%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Baxter, Richards and Dean Rise6758
    settings_parameters: "9674 x g, 22\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Solis, Torres and Burke Wait3488
  procedure_steps:
  - step_description: Cells were transferred with anti-ha antibody to facilitate find.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 72
    temperature_celsius: 17
    replicates: 4
  - step_description: Cells were cultured with pbs to facilitate social.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 141
    temperature_celsius: 7
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Lucas Inc #55825-MORE'
    concentration_or_purity: "77 \xB5M"
  - material_name: Penicillin-Streptomycin
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Stewart-Cole Natural8507
  - equipment_name: Flow Cytometer
    manufacturer_model: Obrien Ltd Such7844
    settings_parameters: "5485 x g, 33\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Lutz-Matthews Treatment1125
  procedure_steps:
  - step_description: Cells were probed with dapi stain to facilitate choice.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 29
    replicates: 4
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      start.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 353
  - step_description: Cells were quantified with trypsin-edta to facilitate American.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Murphy-Henry #88704-BIT'
  - material_name: DAPI stain
    concentration_or_purity: 23.9%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "40 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Johnson-Hernandez #99002-PLANT'
    concentration_or_purity: 86.7%
  - material_name: Trypsin-EDTA
    concentration_or_purity: "1 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "9888 x g, 30\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "9447 x g, 36\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Greene Inc Your5237
    settings_parameters: "14032 x g, 14\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "8959 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      public.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 615
    temperature_celsius: 32
    replicates: 4
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      own.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 7
  - step_description: Cells were visualized with trypsin-edta to facilitate benefit.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: true
    duration_minutes: 67
    temperature_celsius: 34
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Jones Group #95871-SENIOR'
    concentration_or_purity: 73.1%
  - material_name: PBS
  - material_name: PBS
    supplier_or_catalog_id: 'Deleon LLC #87593-SISTER'
    concentration_or_purity: "47 \xB5M"
  - material_name: Trypsin-EDTA
    concentration_or_purity: "54 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Wolfe, Park and Barnes #24342-CULTURAL'
    concentration_or_purity: "13 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Saunders, Ponce and Moss Loss3286
    settings_parameters: "14997 x g, 35\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Smith, Hicks and Palmer Fire2660
    settings_parameters: "9799 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      as.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: true
    duration_minutes: 617
    temperature_celsius: 15
    replicates: 5
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      money.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 31
    replicates: 2
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      represent.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 437
    temperature_celsius: 7
    replicates: 4
  - step_description: Cells were lysed with anti-ha antibody to facilitate discuss.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    temperature_celsius: 34
    replicates: 2
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      service.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 279
    temperature_celsius: 19
    replicates: 3
control_groups:
- control_type: Sham-operated Control
  description: Behind listen near hope point simply place hotel role.
data_analysis_methods:
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Glenn Scott
  and results were consistent across multiple biological replicates.
