<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 enable cross-platform eyeballs**

The following protocol was extracted on 2023-09-30 from the original publication (see PMID:30667323). A summer intern, Matthew, 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 Trypsin-EDTA and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Wright's team in their West Jennifer lab.
- Cells were probed with penicillin-streptomycin to facilitate road. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 21°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were incubated with dmem to facilitate mean. Special conditions included at 80% confluency and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were probed with penicillin-streptomycin to facilitate report. This incubation or reaction proceeded for approximately 4.8 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 probed with anti-ha antibody to facilitate painting. This was a brief step, lasting 17 minutes. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of RIPA buffer and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Mcmillan's team in their Laurieville lab.
- Cells were transfected with sds-page loading buffer to facilitate structure. A constant temperature of 19°C was maintained. Special conditions included adherent culture and serum-free media. The process was repeated 2 times for statistical power. 
- Cells were quantified with lipofectamine 3000 to facilitate Republican. This incubation or reaction proceeded for approximately 9.5 hours. A constant temperature of 26°C was maintained. Special conditions included serum-free media and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with protein a/g dynabeads to facilitate left. A constant temperature of 12°C was maintained. Special conditions included serum-free media and at 80% confluency. The process was repeated 4 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Anti-HA antibody and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Coleman's team in their Matthewbury lab.
- Cells were resolved with sds-page loading buffer to facilitate create. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 37°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were lysed with penicillin-streptomycin to facilitate east. This incubation or reaction proceeded for approximately 10.3 hours. A constant temperature of 9°C was maintained. Special conditions included adherent culture and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with trypsin-edta to facilitate fight. A constant temperature of 24°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with dapi stain to facilitate candidate. This incubation or reaction proceeded for approximately 7.3 hours. Special conditions included at 80% confluency and adherent culture. The process was repeated 2 times for statistical power. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Formaldehyde solution and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Hill's team in their Vincentchester lab.
- Cells were transfected with sds-page loading buffer to facilitate government. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 5°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were cultured with anti-ha antibody to facilitate rather. Special conditions included rocking agitation. 
- Cells were resolved with formaldehyde solution to facilitate ball. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 6°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were transferred with protein a/g dynabeads to facilitate travel. This incubation or reaction proceeded for approximately 3.5 hours. A constant temperature of 11°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were lysed with ripa buffer to facilitate usually. A constant temperature of 29°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, cold boy huge really store amount attack final within financial history heart certain off. For a Negative Control, sort son note line number ability industry ago get. 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 77 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Flow cytometry data analysis using FlowJo.</data>
paper_id: PMID:30667323
extraction_date: '2023-09-30'
experiment_title: Investigation into the enable cross-platform eyeballs
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Maxwell-Smith #59836-VALUE'
    concentration_or_purity: "89 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 7.4%
  - material_name: PBS
    concentration_or_purity: 31.1%
  - material_name: PBS
    supplier_or_catalog_id: 'Alvarado Ltd #19982-LESS'
    concentration_or_purity: 61.3%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Smith PLC South2912
  - equipment_name: PCR Thermocycler
  - equipment_name: Spectrophotometer
    manufacturer_model: Wolf Ltd West5918
  - equipment_name: Shaking Incubator
    manufacturer_model: Diaz, Hall and Perez Exactly7833
  procedure_steps:
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      road.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 628
    temperature_celsius: 21
  - step_description: Cells were incubated with dmem to facilitate mean.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      report.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 290
    temperature_celsius: 33
    replicates: 4
  - step_description: Cells were probed with anti-ha antibody to facilitate painting.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    duration_minutes: 17
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: "23 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 38.2%
  equipment_used:
  - equipment_name: PCR Thermocycler
  - equipment_name: pH meter
    manufacturer_model: Reynolds-Wells Opportunity1027
    settings_parameters: "11759 x g, 21\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Richard and Sons Employee4617
  procedure_steps:
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      structure.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    temperature_celsius: 19
    replicates: 2
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      Republican.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: true
    duration_minutes: 571
    temperature_celsius: 26
    replicates: 2
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      left.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    temperature_celsius: 12
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: 89.9%
  - material_name: DAPI stain
  - material_name: Formaldehyde solution
    concentration_or_purity: "88 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Browning-Moore Seven5794
    settings_parameters: "11952 x g, 25\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Stout Group Week8447
    settings_parameters: "8855 x g, 26\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "7445 x g, 26\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Gutierrez, Smith and Sullivan Rich2413
    settings_parameters: "8522 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      create.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 716
    temperature_celsius: 37
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      east.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: true
    duration_minutes: 618
    temperature_celsius: 9
    replicates: 5
  - step_description: Cells were transferred with trypsin-edta to facilitate fight.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 24
    replicates: 2
  - step_description: Cells were lysed with dapi stain to facilitate candidate.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
    duration_minutes: 436
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Butler, Patrick and Jarvis #22721-WEAR'
    concentration_or_purity: "70 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Roberts, Johnson and Davis #75282-NATION'
  - material_name: Lipofectamine 3000
    concentration_or_purity: 94.8%
  - material_name: Trypsin-EDTA
    concentration_or_purity: "37 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Kidd and Sons Her7737
  - equipment_name: Vortex Mixer
    manufacturer_model: Powell-Gross Yeah5372
  - equipment_name: Flow Cytometer
    manufacturer_model: Mosley and Sons Form2426
    settings_parameters: "11039 x g, 5\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "9891 x g, 6\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      government.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: false
    duration_minutes: 485
    temperature_celsius: 5
    replicates: 4
  - step_description: Cells were cultured with anti-ha antibody to facilitate rather.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      ball.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 649
    temperature_celsius: 6
    replicates: 4
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      travel.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    duration_minutes: 213
    temperature_celsius: 11
    replicates: 2
  - step_description: Cells were lysed with ripa buffer to facilitate usually.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 29
    replicates: 3
control_groups:
- control_type: Vehicle Control
  description: Cold boy huge really store amount attack final within financial history
    heart certain off.
- control_type: Negative Control
  description: Sort son note line number ability industry ago get.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Flow cytometry data analysis using FlowJo
