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Title:          Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease
Subject:        Nature Communications, doi:10.1038/s41467-023-40156-6
Keywords:       
Author:         Alba Garrido-Trigo
Creator:        Springer
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      Title: Macrophage and neutrophil heterogeneity at’single-cell spatial resolution in human inflammatory bowel disease
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       Item: 
        Title: Results
        Destination: A1
        Children: 
         Item: 
          Title: Integration of single-cell RNA sequencing and spatial molecular imaging analysis provides a map of healthy and inflamed colon
          Destination: B1
         Item: 
          Title: Transcriptional analysis at single-cell and spatial resolution reveals different populations of resident and inflammatory macrophages in the colonic mucosa
          Destination: B2
         Item: 
          Title: M0 and M2 represent two independent states
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         Item: 
          Title: Inflammation-associated macrophages, including M1 and Inflammation-Dependent Alternative macrophages, show highly heterogeneous signatures among patients
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         Item: 
          Title: Inflammation-dependent alternative macrophages express neuregulin 1
          Destination: B5
         Item: 
          Title: CosMx Spatial Molecular Imaging analysis confirms the expansion of Inflammation-Dependent Alternative macrophages and’reveals their tissue distribution in inflammatory bowel disease’colon
          Destination: B6
         Item: 
          Title: Inflammatory fibroblasts co-localize with Inflammation-Dependent Alternative macrophages in inflammatory bowel disease
          Destination: B7
         Item: 
          Title: Single-cell RNA sequencing reveals a marked heterogeneity of tissue neutrophils in inflammatory bowel disease colonic mucosa
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        Title: Discussion
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       Item: 
        Title: Methods
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        Children: 
         Item: 
          Title: Patient recruitment and sample collection
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         Item: 
          Title: Human colonic cell isolation for scRNAseq or flow cytometry analysis
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         Item: 
          Title: 10× library preparation and sequencing
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         Item: 
          Title: Single cell data analysis
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         Item: 
          Title: Data processing
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         Item: 
          Title: Identification of cell types
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         Item: 
          Title: Batch correction and cluster annotation
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         Item: 
          Title: Differential abundance testing
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          Title: Trajectory analysis
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         Item: 
          Title: Publicly available scRNAseq datasests
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          Title: CosMx™ spatial molecular imaging (SMI)
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         Item: 
          Title: CosMx™ spatial molecular imager (SMI) sample preparation
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          Title: CosMx Spatial Molecular Imager (SMI) instrument run
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          Title: Segmentation and quality control
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          Title: Preprocessing and feature selection
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          Title: Integration and dimension reduction
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          Title: Cell type annotation
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          Title: Co-localization analysis
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         Item: 
          Title: Mucosal-surface distance calculation
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         Item: 
          Title: Correlation abundance analysis
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         Item: 
          Title: Granulocytes isolation from blood
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         Item: 
          Title: Flow cytometry
          Destination: B30
         Item: 
          Title: Organoid cultures from human colonic crypts and RT-PCR
          Destination: B31
         Item: 
          Title: Bulk RNA-seq analysis of human colonic biopsies
          Destination: B32
         Item: 
          Title: Statistical analysis
          Destination: B33
         Item: 
          Title: Immunohistochemistry (IHC) and immunofluorescence (IF)
          Destination: B34
         Item: 
          Title: Single molecule RNA in’situ hybridization (ISH)
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         Item: 
          Title: Reporting summary
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       Item: 
        Title: Data availability
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       Item: 
        Title: Code availability
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       Item: 
        Title: References
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       Item: 
        Title: Acknowledgements
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       Item: 
        Title: Author contributions
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       Item: 
        Title: Funding
        Destination: A7
       Item: 
        Title: Competing interests
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       Item: 
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               <rdf:li>Alba Garrido-Trigo</rdf:li>
               <rdf:li>Ana M. Corraliza</rdf:li>
               <rdf:li>Marisol Veny</rdf:li>
               <rdf:li>Isabella Dotti</rdf:li>
               <rdf:li>Elisa Melón-Ardanaz</rdf:li>
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               <rdf:li>Sudha Visvanathan</rdf:li>
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   Type: CRC32
  Checksum: 5fe8a4fafc2d9f6d4636ccd203c3ab66
   Type: MD5
  Checksum: 2d1a9f5b88e16b0e163d280add2eb63cc6c0c077
   Type: SHA-1
  Checksum: f864dcd16cdff239f8cf0a4b202e6d7290df9641217e89bbca326f84f61700ab
   Type: SHA-256