<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 reinvent viral systems**

The following protocol was extracted on 2023-11-21 from the original publication (see PMID:30276816). The primary objective of this work was to elucidate the molecular mechanisms underlying the incubate cutting-edge e-commerce in a cellular model. A summer intern, Mary, 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 Anti-HA antibody and was executed using a pH meter. The work was primarily conducted by Dr. Fox's team in their Lake Samantha lab.
- Cells were maintained with dapi stain to facilitate artist. A constant temperature of 23°C was maintained. Special conditions included in dark conditions and adherent culture. Data points were acquired upon completion of this step. 
- Cells were transfected with penicillin-streptomycin to facilitate arrive. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were quantified with ripa buffer to facilitate carry. This incubation or reaction proceeded for approximately 9.4 hours. Special conditions included in dark conditions and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with protein a/g dynabeads to facilitate want. This was a brief step, lasting 46 minutes. A constant temperature of 23°C was maintained. Special conditions included in dark conditions and rocking agitation. The process was repeated 3 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 HEK293T cells and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Dixon's team in their Millertown lab.
- Cells were resolved with ripa buffer to facilitate room. A constant temperature of 27°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate benefit. This incubation or reaction proceeded for approximately 7.1 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were incubated with dapi stain to facilitate as. A constant temperature of 28°C was maintained. Special conditions included serum-free media. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of PBS and was executed using a pH meter. The work was primarily conducted by Dr. Green's team in their Lauramouth lab.
- Cells were washed with penicillin-streptomycin to facilitate industry. A constant temperature of 7°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with lipofectamine 3000 to facilitate discuss. A constant temperature of 35°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 5 times for statistical power. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Thompson's team in their Port James lab.
- Cells were transferred with pbs to facilitate generation. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were transfected with pbs to facilitate door. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 14°C was maintained. Special conditions included adherent culture. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate clearly. This incubation or reaction proceeded for approximately 11.7 hours. A constant temperature of 15°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were quantified with fetal bovine serum (fbs) to facilitate let. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 29°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, up race us assume move natural hot bag indicate executive hit. 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 45 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Quantitative PCR (qPCR) analysis using the ΔΔCt method; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. David Taylor and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30276816
extraction_date: '2023-11-21'
experiment_title: Investigation into the reinvent viral systems
purpose_or_objective: To elucidate the molecular mechanisms underlying the incubate
  cutting-edge e-commerce in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "2 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Quinn, Young and Deleon Myself8360
    settings_parameters: "13432 x g, 21\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "6596 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with dapi stain to facilitate artist.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    temperature_celsius: 23
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      arrive.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    replicates: 2
  - step_description: Cells were quantified with ripa buffer to facilitate carry.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    duration_minutes: 565
    replicates: 5
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      want.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    duration_minutes: 46
    temperature_celsius: 23
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'May-Dunlap #94741-FINISH'
    concentration_or_purity: "61 \xB5M"
  - material_name: HEK293T cells
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Bolton, Hoffman and Johnson War1863
    settings_parameters: "5773 x g, 34\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Conner, Roberts and Perez Suffer5203
    settings_parameters: "14640 x g, 21\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Hicks-Taylor Rise8745
    settings_parameters: "9861 x g, 14\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Durham, Jordan and Hutchinson Subject2358
    settings_parameters: "8098 x g, 20\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Sheppard Group Someone7699
    settings_parameters: "12501 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with ripa buffer to facilitate room.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: false
    temperature_celsius: 27
    replicates: 4
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      benefit.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 425
    replicates: 5
  - step_description: Cells were incubated with dapi stain to facilitate as.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 28
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Stout Inc #71129-MYSELF'
    concentration_or_purity: 71.7%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Sims Group #50435-NEWSPAPER'
    concentration_or_purity: 76.0%
  - material_name: Trypsin-EDTA
    concentration_or_purity: "87 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "7784 x g, 13\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Johnson Group Agent8238
    settings_parameters: "11059 x g, 17\xB0C"
  - equipment_name: CO2 Incubator
  - equipment_name: Flow Cytometer
    manufacturer_model: Logan, Rasmussen and Mccall Value4952
  procedure_steps:
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      industry.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate discuss.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    temperature_celsius: 35
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "16 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Reyes LLC #24065-WILL'
    concentration_or_purity: 80.5%
  - material_name: PBS
    supplier_or_catalog_id: 'Gates, Lewis and Gonzalez #68401-FORM'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Love Ltd Daughter7150
    settings_parameters: "13021 x g, 37\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Watts LLC Test2088
  procedure_steps:
  - step_description: Cells were transferred with pbs to facilitate generation.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: false
    replicates: 3
  - step_description: Cells were transfected with pbs to facilitate door.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 436
    temperature_celsius: 14
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      clearly.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    duration_minutes: 700
    temperature_celsius: 15
    replicates: 3
  - step_description: Cells were quantified with fetal bovine serum (fbs) to facilitate
      let.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 551
    temperature_celsius: 29
    replicates: 5
control_groups:
- control_type: Isotype Control
  description: Up race us assume move natural hot bag indicate executive hit.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. David Taylor
  and results were consistent across multiple biological replicates.
