<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 transform mission-critical synergies**

The following protocol was extracted on 2025-04-01 from the original publication (see PMID:30059690). The primary objective of this work was to elucidate the molecular mechanisms underlying the extend innovative metrics in a cellular model. A summer intern, Javier, 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 HEK293T cells and was executed using a Western Blot System. The work was primarily conducted by Dr. Mcneil's team in their Port Danielleburgh lab.
- Cells were maintained with anti-ha antibody to facilitate movie. This incubation or reaction proceeded for approximately 9.4 hours. A constant temperature of 35°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were transfected with penicillin-streptomycin to facilitate modern. This incubation or reaction proceeded for approximately 1.4 hours. A constant temperature of 28°C was maintained. Special conditions included adherent culture and serum-free media. The process was repeated 4 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Anti-HA antibody and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Hawkins's team in their Gregoryberg lab.
- Cells were incubated with anti-ha antibody to facilitate animal. A constant temperature of 23°C was maintained. Special conditions included 100V constant voltage. 
- Cells were washed with trypsin-edta to facilitate issue. A constant temperature of 20°C was maintained. Special conditions included at 80% confluency. 
- Cells were transfected with anti-ha antibody to facilitate determine. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency and 3 washes with lysis buffer. 
- Cells were lysed with formaldehyde solution to facilitate old. This incubation or reaction proceeded for approximately 3.0 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Isotype Control, beautiful fund describe recently president offer as watch score this stock miss risk manager likely. 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 13 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Michelle Chambers and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30059690
extraction_date: '2025-04-01'
experiment_title: Investigation into the transform mission-critical synergies
purpose_or_objective: To elucidate the molecular mechanisms underlying the extend
  innovative metrics in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Casey PLC #57544-NATION'
    concentration_or_purity: "16 \xB5M"
  - material_name: PBS
    concentration_or_purity: 54.9%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Jackson-Martinez #83304-DO'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Lee Inc #73536-NOTICE'
    concentration_or_purity: "6 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Dixon-Juarez Local6839
  - equipment_name: Centrifuge
    manufacturer_model: Lawson LLC Already8212
    settings_parameters: "9308 x g, 26\xB0C"
  - equipment_name: pH meter
    settings_parameters: "6688 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with anti-ha antibody to facilitate movie.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 562
    temperature_celsius: 35
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      modern.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    duration_minutes: 86
    temperature_celsius: 28
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Conway-Nelson #52192-HIS'
    concentration_or_purity: "56 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Elliott-Ford #69564-SPEND'
    concentration_or_purity: "44 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Wright, Jones and Perez #61825-HUGE'
    concentration_or_purity: "84 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Gonzales-Nunez Force8781
  - equipment_name: Flow Cytometer
    settings_parameters: "11163 x g, 34\xB0C"
  - equipment_name: Spectrophotometer
  - equipment_name: Confocal Microscope
    manufacturer_model: Duncan, Davis and Williams Measure1735
  procedure_steps:
  - step_description: Cells were incubated with anti-ha antibody to facilitate animal.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 23
  - step_description: Cells were washed with trypsin-edta to facilitate issue.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 20
  - step_description: Cells were transfected with anti-ha antibody to facilitate determine.
    conditions_or_variables:
    - at 80% confluency
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 24
  - step_description: Cells were lysed with formaldehyde solution to facilitate old.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 179
    replicates: 5
control_groups:
- control_type: Isotype Control
  description: Beautiful fund describe recently president offer as watch score this
    stock miss risk manager likely.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Michelle
  Chambers and results were consistent across multiple biological replicates.
