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Haley Delamora
Haley-Delamora/
PersonalTherapyStaging
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Development of human pancreatic cancer avatars as a model for dynamic immune landscape profiling and personalised therapy

https://doi.org/10.5061/dryad.qnk98sfr2

Description of the data and file structure

Spatial Transcriptomics files

Spatial transcriptomic datasets are Excel spreadsheets of gene counts from RNAseq analysis which have been normalised using Q3 normalisation. Cellular areas are designated tumours, stroma, or immune by staining for pan-cytokeratin, alpha-smooth actin and DC45, as described in the methods. Column names are the sample names and row names are the gene names. 

The file 'control_ascorbicAcid_metformin_sample_ID_timepoint.xlsx' gives a key to interpret the sample names in the file 'control_ascorbicAcid_metformin_GeoMX' where

  • SegmentLabel = segment designation (tumour, stroma, immune)
  • SegmentDisplayName = the sample name given in 'control_ascorbicAcid_metformin_GeoMX'. 'C' or 'T' at the start of the name represents control and treated samples. The name ends with the segment designation. The rest gives no relevant information.
  • Timepoint = length of time for which the samples have been exposed to metformin and ascorbic acid

The file 'SampleStabilityGeomx_Q3_Norm' is performed on samples which have been designated tumour or stroma only and have not been treated. The data gives the normalised gene counts of samples which have been maintained in the perfusion system for different lengths of time.

  • data is normalised gene counts (normalised using Q3 normalisation) with row names giving gene names in column 1
  • row 1 gives the sample name consisting of: segment designation = tumour or stroma; culture condition = baseline (day 0), perf (perfused) or static (not perfused); DX = number of days for which the section has been maintained (5, 7, 9 or 12); 3-digit identifier
  • row 2 gives the length of time for which the avatar has been maintained in culture in days.

Immune Cell Proximity files

Immune cell proximity study data files are in 9 zipped folders. Each folder corresponds to one of three samples (PDCA 10, 12, 13).

PDCA 10 consists of 2 folders:

  1. PDCA10baseline_proximity-immuneCells_ImmuneCells
  2. PDCA10proximityToTumour_ObjectData

PDCA 12 consists of 5 folders:

  1. PDCA12baseline_proximity-immuneCells_ImmuneCells
  2. PDCA12perfusedDay12_proximity-immuneCells_ImmuneCells
  3. PDCA12perfusedDay12b_proximity-immuneCells_ImmuneCells
  4. PDCA12proximityToTumour_ObjectData
  5. PDCA12staticDay12_proximity-immuneCells_ImmuneCells

PDCA 13 consists of 2 folders:

  1. PDCA13baseline_proximity-immuneCells_ImmuneCells
  2. PDCA13proximityToTumour_ObjectData

Within each folder are 20 CSV files giving distances between two types of cell, given in the name for column H: eg CD4 within 100μm of Macrophage means that in this file the distance of each CD4 cell from all neighbouring macrophages is listed.            

Folder naming convention considerations:

  • The 'proximity_immuneCells_immuneCells' files give data on the distances between each type of immune cell analysed and other proximal immune cells or tumour cells.
  • The 'ObjectData' files give the number of tumour cells within areas of tissue that are predominantly tumour cells ie tumour infiltration.

Within each zipped file is a series of data files for each of the 3 samples at timepoints Day0 (baseline) or Day12. The cell type and proximal cell of interest are given in the column headers.

File naming convention considerations:

  • PTxx = sample PDCAxx
  • BASE = baseline (i.e., day 0)
  • STAT = static culture
  • PERF = perfused culture
  • the rest of the filename gives no important information

Variables:

  • Image location = lab drive identifier. Ignore this
  • Analysis region = lab identifier for the location of tissue slice on the slide
  • Algorithm name = algorithm as defined by HALO software
  • Object id = ID given to the cell pair
  • Cell ID (column E) = ID given to immune cell of interest (macrophage/CD4+ Tcell/CD8+ Tcell/ Treg/B cell)
  • Cell ID (column F)  = ID given to the target cell (macrophage/CD4+ Tcell/CD8+ Tcell/ Treg/B cell/tumour cell)
  • Distance (μm) = distance between the two identified cells in μm
  • macrophage/CD4+ Tcell/CD8+ Tcell/ Treg/B cell within 100um of macrophage/CD4+ Tcell/CD8+ Tcell/ Treg/B cell/tumour cell = '0' if distance  > 100 μm, '1' if distance < 100 μm
  • XMin, XMax, YMin, YMax = coordinates of cell of interest. not used in this analysis

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