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Title:           ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics
Subject:         Genome Biology, 2021, doi:10.1186/s13059-021-02302-5
Keywords:        Single-cell transcriptomics,Planarian,RNA-seq,Fixation,Dissociation,SPLiT-seq,Combinatorial indexing
Author:          Helena García-Castro
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     Item: 
      Title: Abstract
      Destination: sectionAbs1
     Item: 
      Title: Background
      Destination: sectionSec1
     Item: 
      Title: Results
      Destination: sectionSec2
      Children: 
       Item: 
        Title: ACME dissociation produces fixed cells with preserved morphology that can be visualized by flow cytometry
        Destination: sectionSec3
       Item: 
        Title: ACME is a species-versatile method that can be used in a broad range of animals and developmental stages
        Destination: sectionSec4
       Item: 
        Title: ACME-dissociated cells can be cryopreserved multiple times
        Destination: sectionSec5
       Item: 
        Title: ACME-dissociated cells retain high-integrity RNAs
        Destination: sectionSec6
       Item: 
        Title: ACME can be used as a fixative of enzymatic dissociated cells
        Destination: sectionSec7
       Item: 
        Title: Single-cell transcriptomic analysis of cnidarian ACME-dissociated cells using a droplet-based method
        Destination: sectionSec8
       Item: 
        Title: Single-cell transcriptomic analysis of planarian ACME-dissociated cells using combinatorial barcoding
        Destination: sectionSec9
       Item: 
        Title: Cell type composition of two planarian species
        Destination: sectionSec10
       Item: 
        Title: Integration of trypsin-dissociated and ACME-dissociated planarian single-cell datasets
        Destination: sectionSec11
     Item: 
      Title: Discussion
      Destination: sectionSec12
     Item: 
      Title: Conclusions
      Destination: sectionSec13
     Item: 
      Title: Methods
      Destination: sectionSec14
      Children: 
       Item: 
        Title: ACME dissociation
        Destination: sectionSec15
       Item: 
        Title: Protecting RNA from degradation
        Destination: sectionSec16
       Item: 
        Title: Trypsin dissociation
        Destination: sectionSec17
       Item: 
        Title: ACME fixation after trypsin dissociation
        Destination: sectionSec18
       Item: 
        Title: Formaldehyde fixation
        Destination: sectionSec19
       Item: 
        Title: RNA quality assessment and extraction
        Destination: sectionSec20
       Item: 
        Title: Flow cytometry and FACS
        Destination: sectionSec21
       Item: 
        Title: Irradiation
        Destination: sectionSec22
        Children: 
         Item: 
          Title: scRNA-seq of Nematostella vectensis ACME-dissociated cells using 10X Genomics platform
          Destination: sectionSec23
       Item: 
        Title: Cnidarian single-cell transcriptomic analysis
        Destination: sectionSec24
       Item: 
        Title: Split pool ligation-based transcriptome sequencing
        Destination: sectionSec25
        Children: 
         Item: 
          Title: Plate preparation
          Destination: sectionSec26
         Item: 
          Title: Round 1 of barcoding: reverse transcription
          Destination: sectionSec27
         Item: 
          Title: Round 2 of barcoding: ligation 1
          Destination: sectionSec28
         Item: 
          Title: Round 3 of barcoding: ligation 2
          Destination: sectionSec29
         Item: 
          Title: Cell lysis
          Destination: sectionSec30
         Item: 
          Title: cDNA purification with magnetic beads
          Destination: sectionSec31
         Item: 
          Title: Template switch
          Destination: sectionSec32
         Item: 
          Title: PCR amplification
          Destination: sectionSec33
         Item: 
          Title: Size selection
          Destination: sectionSec34
         Item: 
          Title: Tagmentation
          Destination: sectionSec35
         Item: 
          Title: Round 4 of barcoding: PCR
          Destination: sectionSec36
       Item: 
        Title: Planarian single-cell transcriptomic analysis
        Destination: sectionSec37
        Children: 
         Item: 
          Title: Sequencing and quality control
          Destination: sectionSec38
         Item: 
          Title: Read mapping, barcode extraction, and matrix production
          Destination: sectionSec39
         Item: 
          Title: Seurat feature identification, doublet removal, and clustering
          Destination: sectionSec40
         Item: 
          Title: Cluster identity assignment
          Destination: sectionSec41
         Item: 
          Title: Re-mapping of Plass et’al. datasets
          Destination: sectionSec42
         Item: 
          Title: Label transfer and integration
          Destination: sectionSec43
         Item: 
          Title: Other analyses performed for single-cell RNA-seq data
          Destination: sectionSec44
     Item: 
      Title: Supplementary Information
      Destination: sectionSec45
     Item: 
      Title: Acknowledgements
      Destination: section1
     Item: 
      Title: Review history
      Destination: sectionFPar1
     Item: 
      Title: Peer review information
      Destination: sectionFPar2
     Item: 
      Title: Authors’ contributions
      Destination: section2
     Item: 
      Title: Authors’ information
      Destination: sectionFPar4
     Item: 
      Title: Funding
      Destination: section3
     Item: 
      Title: Availability of data and materials
      Destination: section4
     Item: 
      Title: Declarations
      Destination: section5
     Item: 
      Title: Ethics approval and consent to participate
      Destination: sectionFPar5
     Item: 
      Title: Consent for publication
      Destination: sectionFPar6
     Item: 
      Title: Competing interests
      Destination: sectionFPar7
     Item: 
      Title: Author details
      Destination: section6
     Item: 
      Title: References
      Destination: sectionBib1
     Item: 
      Title: Publisher’s Note
      Destination: ArtNote1
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    Author: Helena García-Castro
    Subject: Genome Biology, 2021, doi:10.1186/s13059-021-02302-5
    Keywords: Single-cell transcriptomics,Planarian,RNA-seq,Fixation,Dissociation,SPLiT-seq,Combinatorial indexing
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