Spatial Transcriptomics Reveals Expression Gradients in Developing Wheat Inflorescences at Cellular Resolution

This dataset consists of spatially resolved transcript counts for a selected panel of 300 genes in two near-isogenic lines of wheat. For each near-isogenic line, developing shoot apical meristems at four distinct timepoints were dissected and subjected to the MERFISH protocol developed by VizGen. Details of the approach are in the associated publication.

The dataset is comprised of eight gzipped tar archives (2 genotypes by 4 timepoints).

The genotypes are BC6 near-isogenic lines (NILs) in the UK background Paragon (Triticum aestivum). One NIL carries an introgression on chromosome 7A originating from tetraploid Triticum polonicum. This introgression contains the VRT-A2b allele, which confers elongated glumes and grains. In contrast, the wildtype (WT) NIL carries the VRT-A2a allele.

The timepoints of inflorescence development used here are:

- Early Double Ridge stage (Waddington stage W2)

- Late Double Ridge stage (Waddington stage W2.5)

- Lemma Primordium stage (Waddington stage W3.25)

- Terminal Spikelet stage (Waddington stage W4)

- Carpel Extension stage (Waddington stage W5)

Each archive contains the following:

- The segmented Cellpose2 output for that particular line and timepoint for use within the MERSCOPE program developed by VizGen.

- A folder with the raw data for that particular line and timepoint; (i) a matrix with the detected transcript counts in csv format, (ii) a file detailing the transformation of microns to mosaic pixels in csv format, (iii) a tif image with the raw data output from the DAPI channel, and (iv) a tif image of the raw output of the polyT channel.

- A folder with the processed segmentation output for that particular line and timepoint; (i) a cell-by-gene expression matrix in csv format, (ii) a metadata file for the cells in csv format, (iii) the cellpose2 parquet data in microns, (iv) the cellpose2 parquet data in mosaic pixels, (v) a csv file with the transcript counts for each cell, (vi) a json file with the segmentation specifications, (vii) another folder containing the DAPI and polyT images after manual remvoal of seam lines.

Each of the gzipped tar archive has the same composition.

In addition, the dataset also includes the Metadata information for all samples in hdf5 format (to be used within the MERSCOPE software).