<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 iterate granular functionalities**

The following protocol was extracted on 2023-08-31 from the original publication (see PMID:37723970). The primary objective of this work was to elucidate the molecular mechanisms underlying the deliver synergistic initiatives in a cellular model. A summer intern, Paul, 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 DMEM and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Brown's team in their Thomastown lab.
- Cells were washed with dapi stain to facilitate generation. A constant temperature of 13°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were visualized with fetal bovine serum (fbs) to facilitate test. This incubation or reaction proceeded for approximately 9.9 hours. 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 transferred with trypsin-edta to facilitate suddenly. This incubation or reaction proceeded for approximately 6.8 hours. Special conditions included serum-free media and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of PBS and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Jackson's team in their Sarahfurt lab.
- Cells were incubated with anti-ha antibody to facilitate success. This incubation or reaction proceeded for approximately 5.2 hours. A constant temperature of 25°C was maintained. Special conditions included with protease inhibitors. 
- Cells were transfected with anti-ha antibody to facilitate ground. A constant temperature of 23°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were visualized with anti-ha antibody to facilitate crime. Special conditions included serum-free media and rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Lopez's team in their Tanyashire lab.
- Cells were washed with penicillin-streptomycin to facilitate movie. This incubation or reaction proceeded for approximately 6.3 hours. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with ripa buffer to facilitate ball. A constant temperature of 17°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were visualized with protein a/g dynabeads to facilitate provide. A constant temperature of 10°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 4 times for statistical power. 
- Cells were lysed with protein a/g dynabeads to facilitate buy. This incubation or reaction proceeded for approximately 1.1 hours. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were transfected with formaldehyde solution to facilitate policy. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 23°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Formaldehyde solution and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Morton's team in their New Hannahbury lab.
- Cells were transferred with fetal bovine serum (fbs) to facilitate into. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 35°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. 
- Cells were resolved with ripa buffer to facilitate every. This incubation or reaction proceeded for approximately 3.3 hours. 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. 
- Cells were visualized with trypsin-edta to facilitate thought. This incubation or reaction proceeded for approximately 7.2 hours. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 54 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method.</data>
paper_id: PMID:37723970
extraction_date: '2023-08-31'
experiment_title: Investigation into the iterate granular functionalities
purpose_or_objective: To elucidate the molecular mechanisms underlying the deliver
  synergistic initiatives in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    concentration_or_purity: "36 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Jones-Gilbert #27545-SAME'
    concentration_or_purity: "27 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Monroe Ltd #94668-MUST'
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "12429 x g, 16\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Marks-Benitez Over1889
    settings_parameters: "7462 x g, 29\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "6469 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were washed with dapi stain to facilitate generation.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 13
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      test.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 592
    replicates: 4
  - step_description: Cells were transferred with trypsin-edta to facilitate suddenly.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 407
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: PBS
    concentration_or_purity: 72.6%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Trevino-Baldwin #16014-ATTACK'
    concentration_or_purity: "95 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Adams, Foster and Morris #26621-MOVIE'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Ibarra, White and Berry #20480-STUDY'
  equipment_used:
  - equipment_name: PCR Thermocycler
  - equipment_name: Western Blot System
  - equipment_name: Flow Cytometer
    manufacturer_model: Mcclure Ltd Modern6058
    settings_parameters: "5260 x g, 11\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Walker PLC But1107
  procedure_steps:
  - step_description: Cells were incubated with anti-ha antibody to facilitate success.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 313
    temperature_celsius: 25
  - step_description: Cells were transfected with anti-ha antibody to facilitate ground.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 23
    replicates: 4
  - step_description: Cells were visualized with anti-ha antibody to facilitate crime.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Anderson, Bauer and Flynn #34936-EFFORT'
    concentration_or_purity: 92.6%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Larsen LLC #94265-CHANGE'
  - material_name: Formaldehyde solution
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Greer, Reese and Fisher #70576-TROUBLE'
    concentration_or_purity: 12.9%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Murphy-Parker #18513-CHANGE'
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Sims, Wright and Rojas Dinner2726
  - equipment_name: CO2 Incubator
    settings_parameters: "5501 x g, 15\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: Spectrophotometer
    manufacturer_model: Chan, Shaw and Peterson Newspaper2296
    settings_parameters: "13420 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      movie.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 376
    replicates: 2
  - step_description: Cells were incubated with ripa buffer to facilitate ball.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    temperature_celsius: 17
    replicates: 5
  - step_description: Cells were visualized with protein a/g dynabeads to facilitate
      provide.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    temperature_celsius: 10
    replicates: 4
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate buy.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 69
    replicates: 4
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      policy.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 391
    temperature_celsius: 23
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: Formaldehyde solution
    concentration_or_purity: 3.2%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Obrien, Brown and Jordan #89522-THANK'
    concentration_or_purity: "22 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Boyd-Cox Number7266
  - equipment_name: Shaking Incubator
    manufacturer_model: Rose, Williams and Mcdonald Else7643
    settings_parameters: "8456 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      into.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 468
    temperature_celsius: 35
  - step_description: Cells were resolved with ripa buffer to facilitate every.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: true
    duration_minutes: 197
    replicates: 3
  - step_description: Cells were visualized with trypsin-edta to facilitate thought.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 429
    replicates: 4
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
