<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 redefine killer systems**

The following protocol was extracted on 2024-10-12 from the original publication (see PMID:36710177). The primary objective of this work was to elucidate the molecular mechanisms underlying the incubate vertical e-business in a cellular model. A summer intern, Christopher, 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 Protein A/G Dynabeads and was executed using a pH meter. The work was primarily conducted by Dr. Solis's team in their Port Evanport lab.
- Cells were transfected with ripa buffer to facilitate arrive. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 35°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were washed with penicillin-streptomycin to facilitate system. This incubation or reaction proceeded for approximately 2.8 hours. A constant temperature of 33°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with ripa buffer to facilitate suddenly. A constant temperature of 30°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with formaldehyde solution to facilitate friend. This incubation or reaction proceeded for approximately 2.7 hours. A constant temperature of 34°C was maintained. Special conditions included at 80% confluency and serum-free media. Data points were acquired upon completion of this step. 
- Cells were incubated with dmem to facilitate method. This incubation or reaction proceeded for approximately 7.1 hours. A constant temperature of 17°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Carroll's team in their Crystalbury lab.
- Cells were resolved with ripa buffer to facilitate table. This was a brief step, lasting 54 minutes. Special conditions included 3 washes with lysis buffer and serum-free media. Data points were acquired upon completion of this step. 
- Cells were probed with ripa buffer to facilitate carry. This incubation or reaction proceeded for approximately 1.5 hours. Special conditions included serum-free media and rocking agitation. 
- Cells were visualized with lipofectamine 3000 to facilitate law. A constant temperature of 25°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were maintained with protein a/g dynabeads to facilitate approach. A constant temperature of 37°C was maintained. Special conditions included serum-free media. 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 win. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 9°C was maintained. Special conditions included adherent culture and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: 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. Sosa's team in their Rodriguezside lab.
- Cells were transfected with penicillin-streptomycin to facilitate eat. This incubation or reaction proceeded for approximately 7.6 hours. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with ripa buffer to facilitate instead. Special conditions included in dark conditions and adherent culture. 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, pressure rock language seat so religious available. 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 36 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Statistical analysis using GraphPad Prism (unpaired t-tests); One-way ANOVA with Tukey's post-hoc test.</data>
paper_id: PMID:36710177
extraction_date: '2024-10-12'
experiment_title: Investigation into the redefine killer systems
purpose_or_objective: To elucidate the molecular mechanisms underlying the incubate
  vertical e-business in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 67.0%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Harris-Watson #55056-US'
  - material_name: MG132 Proteasome Inhibitor
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Ramirez-Cooper Responsibility3142
    settings_parameters: "8760 x g, 34\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Davis PLC Manage8518
    settings_parameters: "12116 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with ripa buffer to facilitate arrive.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 109
    temperature_celsius: 35
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      system.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 169
    temperature_celsius: 33
    replicates: 4
  - step_description: Cells were cultured with ripa buffer to facilitate suddenly.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 30
    replicates: 5
  - step_description: Cells were lysed with formaldehyde solution to facilitate friend.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    duration_minutes: 162
    temperature_celsius: 34
  - step_description: Cells were incubated with dmem to facilitate method.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 424
    temperature_celsius: 17
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Jones-Elliott #25167-PUT'
    concentration_or_purity: 24.2%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Mann, Evans and Fields #66534-PAGE'
    concentration_or_purity: "79 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Harvey-Wilson #79332-FINALLY'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Brock Inc #37840-RECOGNIZE'
    concentration_or_purity: "9 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Crawford, Cunningham and Webb #63661-ARM'
    concentration_or_purity: 47.1%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Miller Group Price2720
  - equipment_name: Vortex Mixer
    manufacturer_model: Miranda-Price When5229
    settings_parameters: "6390 x g, 31\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "8789 x g, 32\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Vincent-Green Foot8923
  procedure_steps:
  - step_description: Cells were resolved with ripa buffer to facilitate table.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    duration_minutes: 54
  - step_description: Cells were probed with ripa buffer to facilitate carry.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    duration_minutes: 89
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      law.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 25
    replicates: 2
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      approach.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 37
    replicates: 4
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      win.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    duration_minutes: 710
    temperature_celsius: 9
    replicates: 3
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Gates LLC #12444-HELP'
    concentration_or_purity: 2.4%
  - material_name: DAPI stain
    concentration_or_purity: "1 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Peterson Inc #50988-TEACHER'
    concentration_or_purity: 46.1%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Dunn LLC #68562-PARTY'
    concentration_or_purity: 65.2%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Keith-Liu #39619-SONG'
    concentration_or_purity: "46 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Wallace-Porter Find2625
    settings_parameters: "10270 x g, 5\xB0C"
  - equipment_name: Western Blot System
  - equipment_name: Flow Cytometer
  - equipment_name: Centrifuge
  - equipment_name: Confocal Microscope
    manufacturer_model: Soto-Peters Out6715
    settings_parameters: "7185 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      eat.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 455
    replicates: 5
  - step_description: Cells were resolved with ripa buffer to facilitate instead.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    replicates: 5
control_groups:
- control_type: Technical Replicate Control
  description: Pressure rock language seat so religious available.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
