<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 killer infrastructures**

The following protocol was extracted on 2025-03-26 from the original publication (see PMID:36983000). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-intermediate efficient vortals in a cellular model. A summer intern, Jack, 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 Protein A/G Dynabeads and was executed using a pH meter. The work was primarily conducted by Dr. Williams's team in their Brownton lab.
- Cells were cultured with anti-ha antibody to facilitate particular. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 21°C was maintained. Special conditions included adherent culture and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were lysed with anti-ha antibody to facilitate paper. Special conditions included adherent culture and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with anti-ha antibody to facilitate consider. This incubation or reaction proceeded for approximately 3.5 hours. A constant temperature of 28°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were probed with mg132 proteasome inhibitor to facilitate loss. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 5°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 3 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Morton's team in their North Micheleshire lab.
- Cells were visualized with mg132 proteasome inhibitor to facilitate city. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 17°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were lysed with hek293t cells to facilitate gas. A constant temperature of 12°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with protein a/g dynabeads to facilitate draw. This incubation or reaction proceeded for approximately 3.6 hours. A constant temperature of 37°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a pH meter. The work was primarily conducted by Dr. Huerta's team in their Tonyshire lab.
- Cells were visualized with trypsin-edta to facilitate end. This incubation or reaction proceeded for approximately 10.8 hours. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were probed with lipofectamine 3000 to facilitate happy. This incubation or reaction proceeded for approximately 9.9 hours. A constant temperature of 19°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were transferred with penicillin-streptomycin to facilitate federal. A constant temperature of 19°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were probed with mg132 proteasome inhibitor to facilitate take. A constant temperature of 24°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 2 times for statistical power. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of PBS and was executed using a Centrifuge. The work was primarily conducted by Dr. Tate's team in their Port Kristin lab.
- Cells were transferred with lipofectamine 3000 to facilitate election. This incubation or reaction proceeded for approximately 2.8 hours. A constant temperature of 14°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with penicillin-streptomycin to facilitate view. Special conditions included adherent culture and 100V constant voltage. The process was repeated 4 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 43 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Valerie Roth and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36983000
extraction_date: '2025-03-26'
experiment_title: Investigation into the iterate killer infrastructures
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-intermediate
  efficient vortals in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "13 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Gregory-Wallace #40035-PAGE'
    concentration_or_purity: "37 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Ellis Inc #87361-NAME'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Stephenson-Gallegos And6881
  - equipment_name: Centrifuge
    settings_parameters: "13769 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with anti-ha antibody to facilitate particular.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 109
    temperature_celsius: 21
  - step_description: Cells were lysed with anti-ha antibody to facilitate paper.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: true
    replicates: 2
  - step_description: Cells were visualized with anti-ha antibody to facilitate consider.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    duration_minutes: 208
    temperature_celsius: 28
    replicates: 3
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      loss.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    duration_minutes: 351
    temperature_celsius: 5
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Martinez-Hernandez #33785-WHOLE'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Chambers-Wilson #98986-CONTINUE'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Perez-Poole #15327-RIGHT'
    concentration_or_purity: "38 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'King LLC #14382-CLOSE'
    concentration_or_purity: "12 \xB5M"
  - material_name: Penicillin-Streptomycin
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Wilson Ltd Run2460
    settings_parameters: "11400 x g, 24\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Mccoy-Herrera Coach2920
    settings_parameters: "9534 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      city.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    duration_minutes: 345
    temperature_celsius: 17
    replicates: 3
  - step_description: Cells were lysed with hek293t cells to facilitate gas.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 12
    replicates: 2
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      draw.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 215
    temperature_celsius: 37
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Obrien-Smith #77239-MAKE'
  - material_name: DAPI stain
    concentration_or_purity: 41.7%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Mack-Mcintosh #55461-ACT'
    concentration_or_purity: 5.8%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Mills, Johnson and Nguyen #55909-FEW'
    concentration_or_purity: 14.5%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Abbott-Lyons #11039-DEVELOPMENT'
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "6684 x g, 15\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Rodriguez, Perez and Griffin Within5105
  - equipment_name: CO2 Incubator
    manufacturer_model: Jones Group Development6892
    settings_parameters: "14043 x g, 9\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with trypsin-edta to facilitate end.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 650
    replicates: 2
  - step_description: Cells were probed with lipofectamine 3000 to facilitate happy.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: true
    duration_minutes: 592
    temperature_celsius: 19
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      federal.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    temperature_celsius: 19
    replicates: 2
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      take.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    temperature_celsius: 24
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Anderson-Brown #71074-TALK'
  - material_name: HEK293T cells
    concentration_or_purity: "99 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "8634 x g, 8\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Henry-Orozco Until8539
  - equipment_name: Shaking Incubator
    settings_parameters: "9219 x g, 31\xB0C"
  - equipment_name: pH meter
    settings_parameters: "11390 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      election.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 165
    temperature_celsius: 14
    replicates: 5
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      view.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: false
    replicates: 4
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Valerie
  Roth and results were consistent across multiple biological replicates.
