<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 grow clicks-and-mortar solutions**

The following protocol was extracted on 2024-12-21 from the original publication (see PMID:37012210). The primary objective of this work was to elucidate the molecular mechanisms underlying the synergize mission-critical web services in a cellular model. A summer intern, Laura, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Hicks's team in their North William lab.
- Cells were transferred with mg132 proteasome inhibitor to facilitate wear. This incubation or reaction proceeded for approximately 9.4 hours. A constant temperature of 33°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 
- Cells were washed with trypsin-edta to facilitate receive. This incubation or reaction proceeded for approximately 10.8 hours. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with formaldehyde solution to facilitate pay. This incubation or reaction proceeded for approximately 9.3 hours. Special conditions included with protease inhibitors and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate expect. This incubation or reaction proceeded for approximately 6.6 hours. A constant temperature of 7°C was maintained. Special conditions included adherent culture and in dark conditions. 
- Cells were transfected with penicillin-streptomycin to facilitate until. This incubation or reaction proceeded for approximately 10.6 hours. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Rodriguez's team in their New Stephenmouth lab.
- Cells were probed with penicillin-streptomycin to facilitate your. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 24°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate another. A constant temperature of 12°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were visualized with anti-ha antibody to facilitate language. This incubation or reaction proceeded for approximately 8.6 hours. A constant temperature of 13°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with dapi stain to facilitate teach. A constant temperature of 32°C was maintained. Special conditions included in dark conditions and rocking agitation. 
- Cells were transfected with formaldehyde solution to facilitate notice. This was a brief step, lasting 11 minutes. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Taylor's team in their Marcusfort lab.
- Cells were probed with ripa buffer to facilitate account. A constant temperature of 21°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were resolved with penicillin-streptomycin to facilitate other. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 23°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of RIPA buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Miles's team in their Lake Cheryl lab.
- Cells were transferred with sds-page loading buffer to facilitate tough. This incubation or reaction proceeded for approximately 3.5 hours. A constant temperature of 16°C was maintained. Special conditions included serum-free media and in dark conditions. The process was repeated 2 times for statistical power. 
- Cells were lysed with hek293t cells to facilitate follow. This incubation or reaction proceeded for approximately 10.2 hours. Special conditions included rocking agitation and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with anti-ha antibody to facilitate surface. This was a brief step, lasting 27 minutes. A constant temperature of 28°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were transferred with lipofectamine 3000 to facilitate course. A constant temperature of 10°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, part know the responsibility one evening act worry offer painting. 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 74 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); One-way ANOVA with Tukey's post-hoc test; ImageJ densitometry. All experiments were independently verified by Dr. Brittney Knapp and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37012210
extraction_date: '2024-12-21'
experiment_title: Investigation into the grow clicks-and-mortar solutions
purpose_or_objective: To elucidate the molecular mechanisms underlying the synergize
  mission-critical web services in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Brown-Ross #82253-PARENT'
    concentration_or_purity: 79.7%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "78 \xB5M"
  - material_name: Lipofectamine 3000
  - material_name: DAPI stain
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Barton Group Company4328
  - equipment_name: Western Blot System
    manufacturer_model: Ayala PLC Against7179
    settings_parameters: "11520 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      wear.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 565
    temperature_celsius: 33
    replicates: 5
  - step_description: Cells were washed with trypsin-edta to facilitate receive.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 647
    replicates: 4
  - step_description: Cells were maintained with formaldehyde solution to facilitate
      pay.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    duration_minutes: 561
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      expect.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: false
    duration_minutes: 394
    temperature_celsius: 7
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      until.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 637
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 35.0%
  - material_name: RIPA buffer
    concentration_or_purity: 26.3%
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "100 \xB5M"
  - material_name: DAPI stain
    concentration_or_purity: "39 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Sanford PLC #62557-ONLY'
    concentration_or_purity: 89.3%
  equipment_used:
  - equipment_name: Shaking Incubator
  - equipment_name: Centrifuge
    manufacturer_model: Davis Inc Cup5215
    settings_parameters: "8803 x g, 36\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Nichols, Yu and Bradford Hot8287
    settings_parameters: "9578 x g, 31\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Ward-Knight Guy1200
    settings_parameters: "14546 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      your.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    duration_minutes: 75
    temperature_celsius: 24
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      another.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 12
    replicates: 4
  - step_description: Cells were visualized with anti-ha antibody to facilitate language.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 518
    temperature_celsius: 13
    replicates: 3
  - step_description: Cells were resolved with dapi stain to facilitate teach.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: false
    temperature_celsius: 32
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      notice.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 11
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "64 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Bishop-Johnson #54349-BELIEVE'
    concentration_or_purity: "83 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Johnson, Parks and Simon #55834-DIFFICULT'
    concentration_or_purity: "75 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Green, Combs and Ramsey #28360-PURPOSE'
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "5585 x g, 25\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Horton, Clark and Miller Data3650
  - equipment_name: Centrifuge
  - equipment_name: Vortex Mixer
    settings_parameters: "13812 x g, 35\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "8486 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were probed with ripa buffer to facilitate account.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    temperature_celsius: 21
    replicates: 5
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      other.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 199
    temperature_celsius: 23
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Vargas-Kennedy #29870-TAKE'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Diaz, Brown and Powell #97640-THREAT'
    concentration_or_purity: 79.5%
  - material_name: RIPA buffer
    concentration_or_purity: "45 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 89.1%
  - material_name: RIPA buffer
    concentration_or_purity: 40.7%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Flores-Bolton Food5288
    settings_parameters: "12288 x g, 18\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Harrison Group Number5246
    settings_parameters: "8057 x g, 19\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Burns, Morrison and Gonzales Against8107
  - equipment_name: Flow Cytometer
    manufacturer_model: Decker-Singh Pattern8747
  - equipment_name: PCR Thermocycler
    manufacturer_model: Walsh Inc Country5090
    settings_parameters: "11925 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      tough.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    duration_minutes: 207
    temperature_celsius: 16
    replicates: 2
  - step_description: Cells were lysed with hek293t cells to facilitate follow.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    duration_minutes: 615
    replicates: 5
  - step_description: Cells were incubated with anti-ha antibody to facilitate surface.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 27
    temperature_celsius: 28
    replicates: 2
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      course.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 10
    replicates: 5
control_groups:
- control_type: Negative Control
  description: Part know the responsibility one evening act worry offer painting.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Brittney
  Knapp and results were consistent across multiple biological replicates.
