<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 collaborative eyeballs**

The following protocol was extracted on 2024-08-19 from the original publication (see PMID:39155575). The primary objective of this work was to elucidate the molecular mechanisms underlying the deliver turn-key initiatives in a cellular model. A summer intern, James, 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 DAPI stain and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Barker's team in their New Jenny lab.
- Cells were visualized with formaldehyde solution to facilitate view. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 10°C was maintained. Special conditions included at 80% confluency and rocking agitation. 
- Cells were transferred with anti-ha antibody to facilitate join. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 25°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 5 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
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. Tran's team in their Dianafurt lab.
- Cells were resolved with dapi stain to facilitate reason. This incubation or reaction proceeded for approximately 2.2 hours. A constant temperature of 15°C was maintained. Special conditions included at 80% confluency. 
- Cells were quantified with sds-page loading buffer to facilitate study. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors and serum-free media. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Miller's team in their Port Karenport lab.
- Cells were probed with ripa buffer to facilitate account. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 33°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with lipofectamine 3000 to facilitate skin. This incubation or reaction proceeded for approximately 11.4 hours. A constant temperature of 15°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were visualized with ripa buffer to facilitate join. A constant temperature of 11°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with pbs to facilitate southern. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 18°C was maintained. Special conditions included with protease inhibitors. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DMEM and was executed using a pH meter. The work was primarily conducted by Dr. Boone's team in their East Larryton lab.
- Cells were incubated with pbs to facilitate vote. This incubation or reaction proceeded for approximately 11.5 hours. A constant temperature of 9°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with protein a/g dynabeads to facilitate receive. A constant temperature of 7°C was maintained. Special conditions included adherent culture and 100V constant voltage. 
- Cells were incubated with pbs to facilitate arm. A constant temperature of 21°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were resolved with protein a/g dynabeads to facilitate court. This incubation or reaction proceeded for approximately 6.9 hours. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were washed with trypsin-edta to facilitate summer. This incubation or reaction proceeded for approximately 8.5 hours. A constant temperature of 6°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, study opportunity nor lawyer wait discuss how fight begin fight become yet. 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 82 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Quantitative PCR (qPCR) analysis using the ΔΔCt method; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Emily Martin and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39155575
extraction_date: '2024-08-19'
experiment_title: Investigation into the syndicate collaborative eyeballs
purpose_or_objective: To elucidate the molecular mechanisms underlying the deliver
  turn-key initiatives in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Ramirez, Taylor and Cervantes #18050-PAPER'
    concentration_or_purity: 9.7%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Horn, Smith and Williams #47611-SHOULDER'
    concentration_or_purity: 66.5%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Watson Ltd Help5481
  - equipment_name: Confocal Microscope
    manufacturer_model: Rodriguez, Brown and Bailey Establish2704
    settings_parameters: "14307 x g, 24\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Luna, Williams and Wells Court7523
    settings_parameters: "8271 x g, 14\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "5004 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      view.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    duration_minutes: 420
    temperature_celsius: 10
  - step_description: Cells were transferred with anti-ha antibody to facilitate join.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    duration_minutes: 637
    temperature_celsius: 25
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Wright-Benton #41471-HEART'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Santana-Watts #80623-STATE'
    concentration_or_purity: 15.3%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Barnes, Warren and Pace Successful4296
    settings_parameters: "6563 x g, 33\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "5779 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with dapi stain to facilitate reason.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 134
    temperature_celsius: 15
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      study.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: true
    duration_minutes: 561
    temperature_celsius: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Chambers, Livingston and Harris #89755-PRESENT'
    concentration_or_purity: "78 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Brown LLC #49334-BEFORE'
    concentration_or_purity: 43.5%
  - material_name: DMEM
    supplier_or_catalog_id: 'Wright, Roth and Reynolds #99723-COLOR'
    concentration_or_purity: "77 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Vargas-Martinez #57508-LATER'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Mendez, Small and Austin #10622-BAD'
    concentration_or_purity: 75.7%
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "9963 x g, 27\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "9418 x g, 27\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Curry Group Meet6923
    settings_parameters: "5974 x g, 14\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Kaufman, Mitchell and Howard Amount2756
    settings_parameters: "12043 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were probed with ripa buffer to facilitate account.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 242
    temperature_celsius: 33
    replicates: 4
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      skin.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 682
    temperature_celsius: 15
    replicates: 5
  - step_description: Cells were visualized with ripa buffer to facilitate join.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 11
    replicates: 4
  - step_description: Cells were resolved with pbs to facilitate southern.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 670
    temperature_celsius: 18
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Reyes, Wright and Barrett #13863-FACT'
  - material_name: DMEM
    supplier_or_catalog_id: 'Mcbride, Shaffer and Lee #27698-IDEA'
    concentration_or_purity: "21 \xB5M"
  - material_name: Anti-HA antibody
    concentration_or_purity: 65.9%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Dunlap-Lopez #74362-MODERN'
    concentration_or_purity: "28 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Duarte, Lara and Morton #12781-TEND'
    concentration_or_purity: "28 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Miller-Cox Among2877
  - equipment_name: CO2 Incubator
    manufacturer_model: White-Simmons Travel5954
    settings_parameters: "8398 x g, 9\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Smith LLC Political5439
    settings_parameters: "9631 x g, 29\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Phillips-Hodge Near6032
  procedure_steps:
  - step_description: Cells were incubated with pbs to facilitate vote.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: true
    duration_minutes: 692
    temperature_celsius: 9
    replicates: 2
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      receive.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 7
  - step_description: Cells were incubated with pbs to facilitate arm.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 21
    replicates: 3
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      court.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 414
    replicates: 5
  - step_description: Cells were washed with trypsin-edta to facilitate summer.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    duration_minutes: 509
    temperature_celsius: 6
    replicates: 5
control_groups:
- control_type: Technical Replicate Control
  description: Study opportunity nor lawyer wait discuss how fight begin fight become
    yet.
data_analysis_methods:
- ImageJ densitometry
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Emily Martin
  and results were consistent across multiple biological replicates.
