Dataset DOI: 10.5061/dryad.ffbg79d9d

Description of the data and file structure

This repository hosts datasets describing metrics, time-series imaging-based latent representations, and gene expression derived from mosaic two-dimensional human gastruloids for the following doctorate dissertation thesis: Modeling Chromosomal Mosaicism During Early Human Embryogenesis on Microraft Array Platform (ISBN: 9798241697950).

Files and variables

File: DAMOGOMR.zip

Gastruloid Metadata

Metadata of gastruloid samples isolated for sequencing.

• Plate_Date: date of collection plate
• Well: well address
• Array_Date: date of array (initial culture)
• Condition: euploid or mosaic
• Batch: experimental batch ID
• Raft: microraft index
• Collect: whether gastruloid was successfully collected (0/1 for failure/success)
• RNA: whether gastruloid was successfully sequenced (0/1 for failure/success)

Latent Representations

16-dimensional (16D) latent representations created from TYX stacks (dynamic) from time-series imaging of developing gastruloids derived from cells expressing SOX2-mCitrine reporter.

• batch: experimental batch ID
• condition: euploid or mosaic
• raft: microraft index
• umap_1: UMAP1 values
• umap_2: UMAP2 values

• emb_{n}: latent feature n

  sample_id: {array date}_array{1 or 2}_{raft number}, where array1=euploid and array2=mosaic
  

• split: training (train), validation (val), or test (test) dataset

Bulk RNA-seq

Sequencing data from single euploid and mosaic gastruloids.

• symbol: gene name
• ensemble_ID: ENSEMBL gene ID
• User_ID: gene name
• baseMean: average normalized expression of gene across all samples
• MOSAIC-EUPLOID_log2FC: log base 2 of fold change comparing mosaic to euploid samples
• MOSAIC-EUPLOID_adjPval: adjusted p-value comparing mosaic to euploid samples
• IJ{plate date}{well address}: processed gene counts using DESeq2

• group: upregulated or downregulated
• FDR: false discovery rate
• nGenes: number of genes from input list corresponding to pathway
• Pathway size: total number of genes corresponding to pathway
• Fold Enrichment: fold enrichment of pathway
• Pathway: GO Biological Process term
• URL: URL for GO Biological Process term
• Genes: list of ENSEMBL gene IDs corresponding to genes in pathway

• Gene: gene name
• IJ.{plate date}.{well address}: gene expression count for sample ID

• User_ID: gene name
• ensembl_ID: gene name
• symbol: gene name
• search_label: gene name
• IJ{plate date}{well address}: normalized gene expression count for sample ID

• Cluster: gene expression cluster ID
• Sample: sample ID

• User_ID: gene name
• ensembl_ID: ENSEMBL gene ID
• symbol: gene name
• search_label: {gene name} | {ENSEMBL gene ID}
• IJ{plate date}{well address}: gene expression count normalized by standard deviation for sample ID

• Sample_ID: sample ID
• PC{n}: principal component n value
• Batch: experimental batch ID
• Condition: euploid or mosaic
• Raft: microraft index

• Experimental batch ID and condition (euploid or mosaic) corresponding to each sample ID.

File: DAMOGOMR_Images.zip

Processed

Processed time-series image slices (YX) [{array date}_green_array2_{microraft index}_{time point}.png] of SOX2-mCitrine reporter expressed by living mosaic gastruloids for each time point. Subdirectory names correspond to batch ID.

Raw

Raw time-series image stacks (TCYX) [array2_raft{microraft index}_tl.tif}] of living mosaic gastruloids. Subdirectory names correspond to batch ID.

Channels:

• BF: brightfield (transmitted light)
• SOX2: SOX2-mCitrine

Code/software

For code used, please refer to doi.org/10.5281/zenodo.17073719.