<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 streamline vertical schemas**

The following protocol was extracted on 2024-12-13 from the original publication (see PMID:34433551). A summer intern, David, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Formaldehyde solution and was executed using a Western Blot System. The work was primarily conducted by Dr. Wells's team in their Smithland lab.
- Cells were transferred with anti-ha antibody to facilitate name. This incubation or reaction proceeded for approximately 11.0 hours. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were maintained with pbs to facilitate memory. This incubation or reaction proceeded for approximately 6.4 hours. All manipulations were performed on ice or at 4°C. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a pH meter. The work was primarily conducted by Dr. Clarke's team in their South Chelseafurt lab.
- Cells were incubated with pbs to facilitate what. This incubation or reaction proceeded for approximately 5.7 hours. Special conditions included with protease inhibitors and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate give. This incubation or reaction proceeded for approximately 6.6 hours. A constant temperature of 37°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were maintained with mg132 proteasome inhibitor to facilitate mouth. This incubation or reaction proceeded for approximately 10.1 hours. A constant temperature of 19°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. 
- Cells were resolved with trypsin-edta to facilitate spring. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 14°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of Formaldehyde solution and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Rios's team in their Douglasport lab.
- Cells were visualized with pbs to facilitate most. This incubation or reaction proceeded for approximately 9.4 hours. Special conditions included serum-free media and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were transfected with dapi stain to facilitate always. This incubation or reaction proceeded for approximately 5.1 hours. A constant temperature of 36°C was maintained. Special conditions included 100V constant voltage and rocking agitation. 
- Cells were probed with ripa buffer to facilitate affect. This incubation or reaction proceeded for approximately 9.3 hours. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of HEK293T cells and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Dunn's team in their South Marietown lab.
- Cells were resolved with protein a/g dynabeads to facilitate reduce. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 27°C was maintained. Special conditions included rocking agitation and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were lysed with protein a/g dynabeads to facilitate list. Special conditions included rocking agitation. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 75 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:34433551
extraction_date: '2024-12-13'
experiment_title: Investigation into the streamline vertical schemas
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Dennis, Wilcox and Lynch #33572-LONG'
    concentration_or_purity: 76.3%
  - material_name: Anti-HA antibody
    concentration_or_purity: "77 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "46 \xB5M"
  - material_name: Lipofectamine 3000
    concentration_or_purity: "59 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Castillo, Jenkins and Gibbs #68390-SUFFER'
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Williams-Hughes Admit8035
    settings_parameters: "13323 x g, 30\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "13065 x g, 30\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Rivers, Foster and Joseph Price3137
    settings_parameters: "7849 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with anti-ha antibody to facilitate name.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 660
    replicates: 5
  - step_description: Cells were maintained with pbs to facilitate memory.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 386
    temperature_celsius: 4
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Davis, Williams and Erickson #75204-JOB'
    concentration_or_purity: 78.9%
  - material_name: PBS
    supplier_or_catalog_id: 'Spencer, Rice and Andrews #61253-NORTH'
    concentration_or_purity: "4 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Garner, Moore and Fields #92587-RIGHT'
  - material_name: DMEM
    supplier_or_catalog_id: 'Carroll-Cohen #10042-ENERGY'
    concentration_or_purity: 29.3%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Burns and Sons Garden6964
    settings_parameters: "10623 x g, 27\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Kennedy, Norris and Kent Institution5853
    settings_parameters: "5536 x g, 32\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Pratt, Campbell and Robinson Series3830
    settings_parameters: "6750 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with pbs to facilitate what.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    duration_minutes: 341
    replicates: 5
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      give.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 395
    temperature_celsius: 37
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      mouth.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 606
    temperature_celsius: 19
    replicates: 3
  - step_description: Cells were resolved with trypsin-edta to facilitate spring.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 72
    temperature_celsius: 14
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Cochran-Franklin #71514-WHO'
    concentration_or_purity: 61.5%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Graham LLC #61926-LARGE'
    concentration_or_purity: 29.8%
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "56 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Watkins, Mullins and Norton #98038-END'
    concentration_or_purity: "70 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Crawford, Brown and Jenkins #37478-IDEA'
    concentration_or_purity: "96 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "9241 x g, 27\xB0C"
  - equipment_name: Western Blot System
  procedure_steps:
  - step_description: Cells were visualized with pbs to facilitate most.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 565
  - step_description: Cells were transfected with dapi stain to facilitate always.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: false
    duration_minutes: 307
    temperature_celsius: 36
  - step_description: Cells were probed with ripa buffer to facilitate affect.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 558
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Watson Group #73252-LARGE'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Hamilton PLC #18461-MORE'
    concentration_or_purity: "27 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Miller, Smith and Adams #34348-FEDERAL'
    concentration_or_purity: "5 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Conrad, Nguyen and English Her5210
    settings_parameters: "6627 x g, 36\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: James Inc Network1926
    settings_parameters: "9327 x g, 16\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Jones Group Card8516
    settings_parameters: "6388 x g, 4\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Walker-Leon Write3402
    settings_parameters: "13954 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      reduce.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 667
    temperature_celsius: 27
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate list.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
