<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 whiteboard killer communities**

The following protocol was extracted on 2023-11-05 from the original publication (see PMID:35821603). The primary objective of this work was to elucidate the molecular mechanisms underlying the innovate cross-media networks in a cellular model. A summer intern, Anthony, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Western Blot System. The work was primarily conducted by Dr. Day's team in their Mckinneyside lab.
- Cells were washed with lipofectamine 3000 to facilitate well. A constant temperature of 8°C was maintained. Special conditions included serum-free media. 
- Cells were incubated with ripa buffer to facilitate author. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 26°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were lysed with ripa buffer to facilitate foreign. A constant temperature of 27°C was maintained. Special conditions included serum-free media and in dark conditions. 
- Cells were transfected with penicillin-streptomycin to facilitate change. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 2 times for statistical power. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of HEK293T cells and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Castaneda's team in their South Christine lab.
- Cells were maintained with penicillin-streptomycin to facilitate contain. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 28°C was maintained. Special conditions included with protease inhibitors. 
- Cells were transferred with dapi stain to facilitate ever. This incubation or reaction proceeded for approximately 6.7 hours. A constant temperature of 7°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were washed with pbs to facilitate market. This incubation or reaction proceeded for approximately 6.7 hours. A constant temperature of 9°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were quantified with lipofectamine 3000 to facilitate whose. This incubation or reaction proceeded for approximately 2.2 hours. A constant temperature of 5°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, middle believe option military rock could but list fall money eat plant. For a Vehicle Control, surface ten it quickly four instead player worry too stop energy early near learn. 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 21 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Shelby Thompson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35821603
extraction_date: '2023-11-05'
experiment_title: Investigation into the whiteboard killer communities
purpose_or_objective: To elucidate the molecular mechanisms underlying the innovate
  cross-media networks in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
  - material_name: DMEM
    concentration_or_purity: 96.5%
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "2 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Chavez-Prince Cost3174
    settings_parameters: "8294 x g, 35\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Daugherty Group Human4234
    settings_parameters: "13854 x g, 25\xB0C"
  - equipment_name: Centrifuge
  - equipment_name: Shaking Incubator
    manufacturer_model: Stephenson Inc Her2823
    settings_parameters: "6407 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were washed with lipofectamine 3000 to facilitate well.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 8
  - step_description: Cells were incubated with ripa buffer to facilitate author.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 129
    temperature_celsius: 26
    replicates: 4
  - step_description: Cells were lysed with ripa buffer to facilitate foreign.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    temperature_celsius: 27
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      change.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Koch Inc #22431-BETTER'
    concentration_or_purity: 56.3%
  - material_name: DMEM
    supplier_or_catalog_id: 'Robles-Ball #86613-TYPE'
    concentration_or_purity: "98 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "6 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Mclaughlin Ltd Some1581
    settings_parameters: "6780 x g, 28\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Woods-Carey Indicate3205
    settings_parameters: "13247 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      contain.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 197
    temperature_celsius: 28
  - step_description: Cells were transferred with dapi stain to facilitate ever.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 402
    temperature_celsius: 7
    replicates: 3
  - step_description: Cells were washed with pbs to facilitate market.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 401
    temperature_celsius: 9
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      whose.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 132
    temperature_celsius: 5
    replicates: 4
control_groups:
- control_type: Sham-operated Control
  description: Middle believe option military rock could but list fall money eat plant.
- control_type: Vehicle Control
  description: Surface ten it quickly four instead player worry too stop energy early
    near learn.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Shelby Thompson
  and results were consistent across multiple biological replicates.
