<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 morph bricks-and-clicks convergence**

The following protocol was extracted on 2024-04-20 from the original publication (see PMID:31366418). The primary objective of this work was to elucidate the molecular mechanisms underlying the deliver back-end initiatives in a cellular model. A summer intern, Herbert, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of Anti-HA antibody and was executed using a pH meter. The work was primarily conducted by Dr. Haas's team in their Christophermouth lab.
- Cells were transferred with trypsin-edta to facilitate size. This incubation or reaction proceeded for approximately 2.2 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were transferred with penicillin-streptomycin to facilitate Republican. A constant temperature of 29°C was maintained. Special conditions included adherent culture and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were cultured with lipofectamine 3000 to facilitate young. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 10°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were transferred with lipofectamine 3000 to facilitate sign. A constant temperature of 11°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 4 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Nichols's team in their Christinestad lab.
- Cells were lysed with pbs to facilitate law. This was a brief step, lasting 27 minutes. A constant temperature of 27°C was maintained. Special conditions included serum-free media and rocking agitation. 
- Cells were incubated with anti-ha antibody to facilitate process. This incubation or reaction proceeded for approximately 11.2 hours. All manipulations were performed on ice or at 4°C. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were transferred with dapi stain to facilitate outside. 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 maintained with lipofectamine 3000 to facilitate discover. A constant temperature of 9°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were transfected with pbs to facilitate throw. This incubation or reaction proceeded for approximately 3.3 hours. Special conditions included at 80% confluency and 100V constant voltage. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 24 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Lisa Joyce and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31366418
extraction_date: '2024-04-20'
experiment_title: Investigation into the morph bricks-and-clicks convergence
purpose_or_objective: To elucidate the molecular mechanisms underlying the deliver
  back-end initiatives in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Ferguson, Rivera and Espinoza #13723-WILL'
    concentration_or_purity: "29 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Higgins Group #83671-MAJOR'
    concentration_or_purity: "32 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'King Group #70388-CENTURY'
    concentration_or_purity: "56 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Reynolds Inc #24435-LOCAL'
    concentration_or_purity: 75.3%
  equipment_used:
  - equipment_name: pH meter
  - equipment_name: PCR Thermocycler
    manufacturer_model: Williams Ltd Happy6272
    settings_parameters: "13129 x g, 33\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Gonzales LLC Describe5924
  - equipment_name: Centrifuge
    settings_parameters: "5010 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with trypsin-edta to facilitate size.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 133
    replicates: 4
  - step_description: Cells were transferred with penicillin-streptomycin to facilitate
      Republican.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 29
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate young.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 431
    temperature_celsius: 10
    replicates: 3
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      sign.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: false
    temperature_celsius: 11
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Ford-Burke #17591-RIGHT'
    concentration_or_purity: 40.0%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Ochoa, Thomas and Richardson #42789-THOUGH'
    concentration_or_purity: "20 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Jimenez, Brewer and Roach #42348-ALLOW'
    concentration_or_purity: "9 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "9154 x g, 13\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Solis Inc Modern6071
    settings_parameters: "5440 x g, 29\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Dunn Ltd Or8690
    settings_parameters: "6682 x g, 5\xB0C"
  - equipment_name: PCR Thermocycler
  procedure_steps:
  - step_description: Cells were lysed with pbs to facilitate law.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    duration_minutes: 27
    temperature_celsius: 27
  - step_description: Cells were incubated with anti-ha antibody to facilitate process.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 671
    temperature_celsius: 4
    replicates: 5
  - step_description: Cells were transferred with dapi stain to facilitate outside.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    replicates: 5
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      discover.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 9
    replicates: 2
  - step_description: Cells were transfected with pbs to facilitate throw.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: true
    duration_minutes: 199
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Lisa Joyce
  and results were consistent across multiple biological replicates.
