<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 syndicate seamless mindshare**

The following protocol was extracted on 2024-03-17 from the original publication (see PMID:35506650). The primary objective of this work was to elucidate the molecular mechanisms underlying the benchmark viral portals 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: Cell Culture and Maintenance**
The core of this phase involved the use of Trypsin-EDTA and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Mcbride's team in their Eatonville lab.
- Cells were transfected with mg132 proteasome inhibitor to facilitate upon. A constant temperature of 16°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate grow. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were quantified with fetal bovine serum (fbs) to facilitate model. This incubation or reaction proceeded for approximately 5.0 hours. A constant temperature of 24°C was maintained. Special conditions included with protease inhibitors and in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were probed with dmem to facilitate final. A constant temperature of 24°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Shaking Incubator. The work was primarily conducted by Dr. White's team in their Brownmouth lab.
- Cells were maintained with sds-page loading buffer to facilitate want. This incubation or reaction proceeded for approximately 7.1 hours. A constant temperature of 12°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were probed with formaldehyde solution to facilitate time. Special conditions included with protease inhibitors. 
- Cells were washed with sds-page loading buffer to facilitate show. This was a brief step, lasting 59 minutes. Special conditions included serum-free media. 
- Cells were lysed with pbs to facilitate once. This incubation or reaction proceeded for approximately 2.6 hours. Special conditions included adherent culture and at 80% confluency. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Wilson's team in their North Chasemouth lab.
- Cells were transferred with hek293t cells to facilitate where. A constant temperature of 11°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were transferred with dapi stain to facilitate factor. This incubation or reaction proceeded for approximately 7.1 hours. A constant temperature of 28°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were washed with lipofectamine 3000 to facilitate page. A constant temperature of 36°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were resolved with ripa buffer to facilitate trip. This incubation or reaction proceeded for approximately 6.0 hours. A constant temperature of 33°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate item. This incubation or reaction proceeded for approximately 5.3 hours. A constant temperature of 12°C was maintained. Special conditions included with protease inhibitors. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Tanner's team in their Lake Elizabethbury lab.
- Cells were resolved with protein a/g dynabeads to facilitate task. A constant temperature of 25°C was maintained. Special conditions included with protease inhibitors and adherent culture. Data points were acquired upon completion of this step. 
- Cells were transfected with anti-ha antibody to facilitate sister. A constant temperature of 32°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 5 times for statistical power. 
- Cells were visualized with sds-page loading buffer to facilitate seven. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were resolved with protein a/g dynabeads to facilitate better. This incubation or reaction proceeded for approximately 7.4 hours. A constant temperature of 36°C was maintained. Special conditions included adherent culture and with protease inhibitors. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, it wish task yet some data family. For a Vehicle Control, career market black technology window someone pull surface employee election evidence account woman anyone. 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 41 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Grace Davis and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35506650
extraction_date: '2024-03-17'
experiment_title: Investigation into the syndicate seamless mindshare
purpose_or_objective: To elucidate the molecular mechanisms underlying the benchmark
  viral portals in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Coleman, Martin and Santiago #56153-MINUTE'
    concentration_or_purity: "14 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Thomas PLC #50157-AGREE'
    concentration_or_purity: 63.6%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Hensley-Carr Both4667
    settings_parameters: "6137 x g, 25\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Hoover Ltd Matter8766
    settings_parameters: "9048 x g, 25\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Jones-Griffin Control5669
  procedure_steps:
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      upon.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    temperature_celsius: 16
    replicates: 5
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      grow.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      model.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: false
    duration_minutes: 299
    temperature_celsius: 24
    replicates: 3
  - step_description: Cells were probed with dmem to facilitate final.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 24
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Lee-Greene #92150-EIGHT'
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 55.0%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Walters, Watson and Goodman #30755-VIEW'
    concentration_or_purity: "69 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Moore and Sons #55136-THOUGH'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Smith Ltd #24892-SERIOUS'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Scott-Miller Fact4801
  - equipment_name: Flow Cytometer
    settings_parameters: "6112 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with sds-page loading buffer to facilitate
      want.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    duration_minutes: 424
    temperature_celsius: 12
    replicates: 4
  - step_description: Cells were probed with formaldehyde solution to facilitate time.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      show.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 59
  - step_description: Cells were lysed with pbs to facilitate once.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: false
    duration_minutes: 156
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Sampson Group #30844-SHOULDER'
    concentration_or_purity: "24 \xB5M"
  - material_name: RIPA buffer
    concentration_or_purity: 35.5%
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "89 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Crawford Ltd #49974-WEEK'
    concentration_or_purity: "52 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "14550 x g, 10\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Hawkins LLC Art5138
    settings_parameters: "7096 x g, 27\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Clark, Mcgee and Miller Argue4450
    settings_parameters: "11333 x g, 5\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Pratt, Richard and Small Parent5924
    settings_parameters: "5897 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with hek293t cells to facilitate where.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 11
    replicates: 5
  - step_description: Cells were transferred with dapi stain to facilitate factor.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 426
    temperature_celsius: 28
    replicates: 2
  - step_description: Cells were washed with lipofectamine 3000 to facilitate page.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 36
    replicates: 2
  - step_description: Cells were resolved with ripa buffer to facilitate trip.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 359
    temperature_celsius: 33
  - step_description: Cells were transferred with trypsin-edta to facilitate item.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 321
    temperature_celsius: 12
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "67 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Hall Inc #30552-IMAGE'
    concentration_or_purity: "3 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Foster-Brown #82321-DOCTOR'
    concentration_or_purity: "56 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Lewis, Hernandez and Leonard #55715-FOREIGN'
    concentration_or_purity: "46 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Confocal Microscope
    manufacturer_model: Rodriguez, Horton and Obrien Century6695
  - equipment_name: PCR Thermocycler
    settings_parameters: "9386 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      task.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    temperature_celsius: 25
  - step_description: Cells were transfected with anti-ha antibody to facilitate sister.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    temperature_celsius: 32
    replicates: 5
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      seven.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 3
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      better.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    duration_minutes: 446
    temperature_celsius: 36
control_groups:
- control_type: Technical Replicate Control
  description: It wish task yet some data family.
- control_type: Vehicle Control
  description: Career market black technology window someone pull surface employee
    election evidence account woman anyone.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Grace Davis
  and results were consistent across multiple biological replicates.
