Murine spleen CODEX dataset (30 antibodies, 3 BALBc spleens, 6 MRL/lpr spleens)



For any question regarding this database please contact Yury Goltsev (goltsev at stanford.edu) or Nikolay Samusik (samusik at stanford.edu)



Manuscript

Deep profiling of mouse splenic architecture with CODEX multiplexed imaging.

Yury Goltsev, Nikolay Samusik, Julia Kennedy-Darling, Salil Bhate, Matthew Hale, Gustavo Vazquez, Sarah Black and Garry Nolan

Dataset files and additional information

CSV file contains mean marker intensities and X, Y, Z corrdinates for each cell relative to the top left corner of its tile.
Tile IDs correspond to tile images sorted in the alphanumeric order
Size parameter corresponds to the cell object sizes in voxels
"imaging phenotype Cluster ID" column specifies the phenotypic cluster identity as determined by X-shift
"niche Cluster ID" column specifies the i-niche cluster determined by K-means (K=100)
neighborhood graph files describes which pairs of cells are adjacent to one another

CODEX_MRLdataset_expression.csv
CODEX_MRLdataset_neighborhood_graph.csv
Additional examples of cell passports - related to FIgure S2
Additional examples of interacting cells - related to Figure S5
channelNames_BALBcMRLdataset.txt
BALBcMRLdataset_exposuretimes.csv


Supplementary Materials and Methods

Supplementary Materials and Methods

SOFTWARE

Software used in the paper for parsing the data can be obtained at
this github link

Single antibody stain validation database

A combined TIFF stack showing single stains with pairs of CODEX antibodies (Cy3 and Cy5 channels) counterstained with B220-FITC.
This data was collected for validation of conjugate antigen specificity.

combined_antibody_testing.tif


CODEX Cell spread vs CyTOF comparison - mouse spleen - FCS files

CODEX_CellSpread_UQ_bgSub_Cleanup.fcs
Mouse_Spleen_CyTOF_normalized_Singlets.fcs


Links to CYTOBANK experiments with gating and scaling information

CyTOF on isolated splenocytes (Fig.2B)
CODEX on spread isolated cplenocytes (Fig.2B)
CODEX on BALBc spleen tissue sections, effect of lateral bleed compensation (Fig.2E)


FCS files

FCS files contain mean marker intensities and X, Y, Z corrdinates for each cell relative to the top left corner of its tile.
Tile IDs correspond to tile images sorted in a alphanumeric order
Size parameter corresponds to the cell object size in voxels
ClusterID column specifies the phenotypic cluster identity as determined by X-shift

BALBc-1.fcs
BALBc-2.fcs
BALBc-3.fcs
MRL-4.fcs
MRL-5.fcs
MRL-6.fcs
MRL-7.fcs
MRL-8.fcs
MRL-9.fcs
ClusterIDtoName.txt : mapping of clusterID (a column in FCS files) to cell types. Unmapped ClusterIDs are considered to be debris.

Images (best viewed using FIJI)

Stitched image hyperstacks (best-focused plane, downsampled 0.2x, 940nm/pixel)

BALBc-slide1/BALBc-1_Fused.tif
BALBc-slide1/BALBc-2_Fused.tif
BALBc-slide1/BALBc-3_Fused.tif
MRL-slide2/MRL-4_Fused.tif
MRL-slide2/MRL-8_Fused.tif
MRL-slide2/MRL-9_Fused.tif
MRL-slide3/MRL-5_Fused.tif
MRL-slide3/MRL-6_Fused.tif
MRL-slide3/MRL-7_Fused.tif

Tissue morphology maps (BALBc only)

BALBc-1_Map.tif
BALBc-2_Map.tif
BALBc-3_Map.tif

Voronoi diagrams of cell type distributions

BALBc-1_VoronoiDiagram.png
BALBc-2_VoronoiDiagram.png
BALBc-3_VoronoiDiagram.png
MRL-4_VoronoiDiagram.png
MRL-5_VoronoiDiagram.png
MRL-6_VoronoiDiagram.png
MRL-7_VoronoiDiagram.png
MRL-8_VoronoiDiagram.png
MRL-9_VoronoiDiagram.png
Legend (same for all tissues)

Deconvolved Z-stacks (xres=188nm, yres=188nm, zres=900nm):

BALBc-slide1

BALBc-1
X01_Y01
X01_Y02
X01_Y03
X01_Y04
X01_Y05
X01_Y06
X01_Y07
X01_Y08
X01_Y09
X02_Y01
X02_Y02
X02_Y03
X02_Y04
X02_Y05
X02_Y06
X02_Y07
X02_Y08
X02_Y09
X03_Y01
X03_Y02
X03_Y03
X03_Y04
X03_Y05
X03_Y06
X03_Y07
X03_Y08
X03_Y09
X04_Y01
X04_Y02
X04_Y03
X04_Y04
X04_Y05
X04_Y06
X04_Y07
X04_Y08
X04_Y09
X05_Y01
X05_Y02
X05_Y03
X05_Y04
X05_Y05
X05_Y06
X05_Y07
X05_Y08
X05_Y09
X06_Y01
X06_Y02
X06_Y03
X06_Y04
X06_Y05
X06_Y06
X06_Y07
X06_Y08
X06_Y09
X07_Y01
X07_Y02
X07_Y03
X07_Y04
X07_Y05
X07_Y06
X07_Y07
X07_Y08
X07_Y09
BALBc-2
X01_Y01
X01_Y02
X01_Y03
X01_Y04
X01_Y05
X01_Y06
X01_Y07
X01_Y08
X01_Y09
X02_Y01
X02_Y02
X02_Y03
X02_Y04
X02_Y05
X02_Y06
X02_Y07
X02_Y08
X02_Y09
X03_Y01
X03_Y02
X03_Y03
X03_Y04
X03_Y05
X03_Y06
X03_Y07
X03_Y08
X03_Y09
X04_Y01
X04_Y02
X04_Y03
X04_Y04
X04_Y05
X04_Y06
X04_Y07
X04_Y08
X04_Y09
X05_Y01
X05_Y02
X05_Y03
X05_Y04
X05_Y05
X05_Y06
X05_Y07
X05_Y08
X05_Y09
X06_Y01
X06_Y02
X06_Y03
X06_Y04
X06_Y05
X06_Y06
X06_Y07
X06_Y08
X06_Y09
X07_Y01
X07_Y02
X07_Y03
X07_Y04
X07_Y05
X07_Y06
X07_Y07
X07_Y08
X07_Y09
BALBc-3
X01_Y01
X01_Y02
X01_Y03
X01_Y04
X01_Y05
X01_Y06
X01_Y07
X01_Y08
X01_Y09
X02_Y01
X02_Y02
X02_Y03
X02_Y04
X02_Y05
X02_Y06
X02_Y07
X02_Y08
X02_Y09
X03_Y01
X03_Y02
X03_Y03
X03_Y04
X03_Y05
X03_Y06
X03_Y07
X03_Y08
X03_Y09
X04_Y01
X04_Y02
X04_Y03
X04_Y04
X04_Y05
X04_Y06
X04_Y07
X04_Y08
X04_Y09
X05_Y01
X05_Y02
X05_Y03
X05_Y04
X05_Y05
X05_Y06
X05_Y07
X05_Y08
X05_Y09
X06_Y01
X06_Y02
X06_Y03
X06_Y04
X06_Y05
X06_Y06
X06_Y07
X06_Y08
X06_Y09
X07_Y01
X07_Y02
X07_Y03
X07_Y04
X07_Y05
X07_Y06
X07_Y07
X07_Y08
X07_Y09

MRL-slide2

MRL-4
X01_Y01
X01_Y02
X01_Y03
X01_Y04
X01_Y05
X01_Y06
X01_Y07
X01_Y08
X01_Y09
X02_Y01
X02_Y02
X02_Y03
X02_Y04
X02_Y05
X02_Y06
X02_Y07
X02_Y08
X02_Y09
X03_Y01
X03_Y02
X03_Y03
X03_Y04
X03_Y05
X03_Y06
X03_Y07
X03_Y08
X03_Y09
X04_Y01
X04_Y02
X04_Y03
X04_Y04
X04_Y05
X04_Y06
X04_Y07
X04_Y08
X04_Y09
X05_Y01
X05_Y02
X05_Y03
X05_Y04
X05_Y05
X05_Y06
X05_Y07
X05_Y08
X05_Y09
X06_Y01
X06_Y02
X06_Y03
X06_Y04
X06_Y05
X06_Y06
X06_Y07
X06_Y08
X06_Y09
X07_Y01
X07_Y02
X07_Y03
X07_Y04
X07_Y05
X07_Y06
X07_Y07
X07_Y08
X07_Y09
MRL-8
X01_Y01
X01_Y02
X01_Y03
X01_Y04
X01_Y05
X01_Y06
X01_Y07
X01_Y08
X01_Y09
X02_Y01
X02_Y02
X02_Y03
X02_Y04
X02_Y05
X02_Y06
X02_Y07
X02_Y08
X02_Y09
X03_Y01
X03_Y02
X03_Y03
X03_Y04
X03_Y05
X03_Y06
X03_Y07
X03_Y08
X03_Y09
X04_Y01
X04_Y02
X04_Y03
X04_Y04
X04_Y05
X04_Y06
X04_Y07
X04_Y08
X04_Y09
X05_Y01
X05_Y02
X05_Y03
X05_Y04
X05_Y05
X05_Y06
X05_Y07
X05_Y08
X05_Y09
X06_Y01
X06_Y02
X06_Y03
X06_Y04
X06_Y05
X06_Y06
X06_Y07
X06_Y08
X06_Y09
X07_Y01
X07_Y02
X07_Y03
X07_Y04
X07_Y05
X07_Y06
X07_Y07
X07_Y08
X07_Y09
MRL-9
X01_Y01
X01_Y02
X01_Y03
X01_Y04
X01_Y05
X01_Y06
X01_Y07
X01_Y08
X01_Y09
X02_Y01
X02_Y02
X02_Y03
X02_Y04
X02_Y05
X02_Y06
X02_Y07
X02_Y08
X02_Y09
X03_Y01
X03_Y02
X03_Y03
X03_Y04
X03_Y05
X03_Y06
X03_Y07
X03_Y08
X03_Y09
X04_Y01
X04_Y02
X04_Y03
X04_Y04
X04_Y05
X04_Y06
X04_Y07
X04_Y08
X04_Y09
X05_Y01
X05_Y02
X05_Y03
X05_Y04
X05_Y05
X05_Y06
X05_Y07
X05_Y08
X05_Y09
X06_Y01
X06_Y02
X06_Y03
X06_Y04
X06_Y05
X06_Y06
X06_Y07
X06_Y08
X06_Y09
X07_Y01
X07_Y02
X07_Y03
X07_Y04
X07_Y05
X07_Y06
X07_Y07
X07_Y08
X07_Y09

MRL-slide3

MRL-5
X01_Y01
X01_Y02
X01_Y03
X01_Y04
X01_Y05
X01_Y06
X01_Y07
X01_Y08
X01_Y09
X02_Y01
X02_Y02
X02_Y03
X02_Y04
X02_Y05
X02_Y06
X02_Y07
X02_Y08
X02_Y09
X03_Y01
X03_Y02
X03_Y03
X03_Y04
X03_Y05
X03_Y06
X03_Y07
X03_Y08
X03_Y09
X04_Y01
X04_Y02
X04_Y03
X04_Y04
X04_Y05
X04_Y06
X04_Y07
X04_Y08
X04_Y09
X05_Y01
X05_Y02
X05_Y03
X05_Y04
X05_Y05
X05_Y06
X05_Y07
X05_Y08
X05_Y09
X06_Y01
X06_Y02
X06_Y03
X06_Y04
X06_Y05
X06_Y06
X06_Y07
X06_Y08
X06_Y09
X07_Y01
X07_Y02
X07_Y03
X07_Y04
X07_Y05
X07_Y06
X07_Y07
X07_Y08
X07_Y09
MRL-6
X01_Y01
X01_Y02
X01_Y03
X01_Y04
X01_Y05
X01_Y06
X01_Y07
X01_Y08
X01_Y09
X02_Y01
X02_Y02
X02_Y03
X02_Y04
X02_Y05
X02_Y06
X02_Y07
X02_Y08
X02_Y09
X03_Y01
X03_Y02
X03_Y03
X03_Y04
X03_Y05
X03_Y06
X03_Y07
X03_Y08
X03_Y09
X04_Y01
X04_Y02
X04_Y03
X04_Y04
X04_Y05
X04_Y06
X04_Y07
X04_Y08
X04_Y09
X05_Y01
X05_Y02
X05_Y03
X05_Y04
X05_Y05
X05_Y06
X05_Y07
X05_Y08
X05_Y09
X06_Y01
X06_Y02
X06_Y03
X06_Y04
X06_Y05
X06_Y06
X06_Y07
X06_Y08
X06_Y09
X07_Y01
X07_Y02
X07_Y03
X07_Y04
X07_Y05
X07_Y06
X07_Y07
X07_Y08
X07_Y09
MRL-7
X01_Y01
X01_Y02
X01_Y03
X01_Y04
X01_Y05
X01_Y06
X01_Y07
X01_Y08
X01_Y09
X02_Y01
X02_Y02
X02_Y03
X02_Y04
X02_Y05
X02_Y06
X02_Y07
X02_Y08
X02_Y09
X03_Y01
X03_Y02
X03_Y03
X03_Y04
X03_Y05
X03_Y06
X03_Y07
X03_Y08
X03_Y09
X04_Y01
X04_Y02
X04_Y03
X04_Y04
X04_Y05
X04_Y06
X04_Y07
X04_Y08
X04_Y09
X05_Y01
X05_Y02
X05_Y03
X05_Y04
X05_Y05
X05_Y06
X05_Y07
X05_Y08
X05_Y09
X06_Y01
X06_Y02
X06_Y03
X06_Y04
X06_Y05
X06_Y06
X06_Y07
X06_Y08
X06_Y09
X07_Y01
X07_Y02
X07_Y03
X07_Y04
X07_Y05
X07_Y06
X07_Y07
X07_Y08
X07_Y09