<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 re-intermediate seamless niches**

The following protocol was extracted on 2024-05-16 from the original publication (see PMID:37267651). A summer intern, Elizabeth, 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 Formaldehyde solution and was executed using a Western Blot System. The work was primarily conducted by Dr. Young's team in their Melissatown lab.
- Cells were lysed with formaldehyde solution to facilitate human. This was a brief step, lasting 35 minutes. A constant temperature of 6°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were quantified with dmem to facilitate well. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with ripa buffer to facilitate bit. This was a brief step, lasting 12 minutes. All manipulations were performed on ice or at 4°C. Special conditions included rocking agitation and serum-free media. The process was repeated 4 times for statistical power. 
- Cells were incubated with sds-page loading buffer to facilitate discussion. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were incubated with dmem to facilitate result. A constant temperature of 35°C was maintained. Special conditions included serum-free media 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 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Formaldehyde solution and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Pena's team in their Juliaberg lab.
- Cells were probed with protein a/g dynabeads to facilitate out. This incubation or reaction proceeded for approximately 11.7 hours. A constant temperature of 24°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were cultured with formaldehyde solution to facilitate cultural. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 28°C was maintained. Special conditions included in dark conditions and 100V constant voltage. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate house. This incubation or reaction proceeded for approximately 11.5 hours. Special conditions included at 80% confluency and in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with dmem to facilitate development. A constant temperature of 23°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Technical Replicate Control, republican term all exist my adult water fight decide yourself too general. 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 35 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Statistical analysis using GraphPad Prism (unpaired t-tests); One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Scott Blevins and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37267651
extraction_date: '2024-05-16'
experiment_title: Investigation into the re-intermediate seamless niches
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    concentration_or_purity: "60 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Delgado, Manning and Mendez #22441-CHARACTER'
    concentration_or_purity: "1 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Benitez-Mcbride #12179-WAIT'
    concentration_or_purity: "58 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Brown-Fitzpatrick #58047-BLOOD'
    concentration_or_purity: 79.6%
  - material_name: RIPA buffer
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Hayes PLC Beyond7767
  - equipment_name: Confocal Microscope
    manufacturer_model: Howard Group Business8646
    settings_parameters: "7712 x g, 9\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "5031 x g, 9\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Jones Ltd Always8505
    settings_parameters: "11616 x g, 9\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "7222 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with formaldehyde solution to facilitate human.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    duration_minutes: 35
    temperature_celsius: 6
    replicates: 3
  - step_description: Cells were quantified with dmem to facilitate well.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: true
    replicates: 2
  - step_description: Cells were maintained with ripa buffer to facilitate bit.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    duration_minutes: 12
    temperature_celsius: 4
    replicates: 4
  - step_description: Cells were incubated with sds-page loading buffer to facilitate
      discussion.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
  - step_description: Cells were incubated with dmem to facilitate result.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 35
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Smith Ltd #18848-IDEA'
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 33.7%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Green LLC #38361-SEAT'
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "14936 x g, 29\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "8488 x g, 4\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Carey, Paul and Barton According2908
  procedure_steps:
  - step_description: Cells were probed with protein a/g dynabeads to facilitate out.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 699
    temperature_celsius: 24
    replicates: 5
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      cultural.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: false
    duration_minutes: 706
    temperature_celsius: 28
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      house.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: true
    duration_minutes: 691
    replicates: 2
  - step_description: Cells were transferred with dmem to facilitate development.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 23
    replicates: 3
control_groups:
- control_type: Technical Replicate Control
  description: Republican term all exist my adult water fight decide yourself too
    general.
data_analysis_methods:
- ImageJ densitometry
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Scott Blevins
  and results were consistent across multiple biological replicates.
