keller-mark/contributors.tsv Secret

## contributors.tsv

          
            version
            affiliation
            first_name
            last_name
            middle_name_or_initial
            name
            orcid_id
            is_contact

            
              1
              Harvard Medical School
              Mark
              Keller
              S
              Mark S Keller
              0000-0003-3003-874X
              FALSE

            
              Harvard Medical School
              Ilan
              Gold
              
              Ilan Gold
              0000-0002-5823-1026
              FALSE

            
              Harvard Medical School
              Chuck
              McCallum
              
              Chuck McCallum
              0000-0003-4039-9768
              FALSE

            
              Harvard Medical School
              Trevor
              Manz
              
              Trevor Manz
              0000-0001-7694-5164
              FALSE

            
              Harvard Medical School
              Peter
              Kharchenko
              V
              Peter V Kharchenko
              0000-0002-6036-5875
              FALSE

            
              Harvard Medical School
              Nils
              Gehlenborg
              
              Nils Gehlenborg
              0000-0003-0327-8297
              TRUE

## description.md

      
    Raw
  

              description.md
            
          
    name
    Use Case 1
  
  
    figures
    
  
  name
  file
  
  
  Visualization
  vitessce.json
  
  
Single-molecule fluorescence in situ hybridization from the mouse somatosensory cortex

Codeluppi et al. used single-molecule fluorescence in situ hybridization (smFISH) to profile the somatosensory cortex in a mouse brain section (Nature Methods 2018). The authors selected 33 marker genes based on previous scRNA-seq findings in the somatosensory cortex and their ability to define cell types. A notable finding from this experiment was the discovery of a transition region defined by the Pyramidal L3/4 excitatory neuron cell type. Using the spatial plot and heatmap in Vitessce, we can reproduce this finding and observe the reported joint expression of markers Lamp5 and Rorb that define the surrounding Pyramidal L2/3 and L4 cell types, respectively.

  
## metadata.tsv

          
            version
            assay_type
            contributors_path
            data_path

            
              0
              Publication
              extras/contributors.tsv
              .
version	affiliation	first_name	last_name	middle_name_or_initial	name	orcid_id	is_contact
1	Harvard Medical School	Mark	Keller	S	Mark S Keller	0000-0003-3003-874X	FALSE
	Harvard Medical School	Ilan	Gold		Ilan Gold	0000-0002-5823-1026	FALSE
	Harvard Medical School	Chuck	McCallum		Chuck McCallum	0000-0003-4039-9768	FALSE
	Harvard Medical School	Trevor	Manz		Trevor Manz	0000-0001-7694-5164	FALSE
	Harvard Medical School	Peter	Kharchenko	V	Peter V Kharchenko	0000-0002-6036-5875	FALSE
	Harvard Medical School	Nils	Gehlenborg		Nils Gehlenborg	0000-0003-0327-8297	TRUE
	version	assay_type	contributors_path	data_path
	0	Publication	extras/contributors.tsv	.