Where can I find the single cell RNAseq count data for each slice?

[cristalliao]

Dear Professor,

I have a question how can I use the 6.5 PCW human embryonic heart dataset in another Model? For example, I want to use the CARD technique, it requires two types of input data:

1. spatial transcriptomics count data, along with spatial location information.
2. single cell RNAseq (scRNA-seq) count data, along with meta information indicating the cell type information and the sample (subject) information for each cell.

For example, I want to use slice 0 data in the 6.5 PCW human embryonic heart dataset to implement the CARD technique. Right now, I can find the first dataset: spatial transcriptomics count data, along with spatial location information. I just save the dataset from the data cleaning part of STitch3D in Example 2 in Python, and then read it in R:

However, I cannot find the single-cell RNAseq (scRNA-seq) count data, along with meta information indicating the cell type information and the sample (subject) information for each cell, for slice 0 in the 6.5 PCW human embryonic heart dataset.

This is an example in the CARD paper:

I also what to find this type of information for slice 0, which has 39,525 × 100 dimensions for single-cell RNAseq (scRNA-seq) count data, along with meta information indicating the cell type information and the sample (subject) information for each cell.

Do you have any suggestions to find this data? Where can I find it?

Thanks in advance!

[gefeiwang]

Hi Cristal,

There is not a single-cell RNA-seq reference dataset for slice0 specifically. You can use the entire scRNA-seq dataset as the cell-type reference data for all slices.

Best, Gefei

[cristalliao]

Dear Professor Geifei,

Thanks for your reply! I was wondering how to produce the figure in this great STitch3D paper. It seems like Figures 5j and 5k are based on only one slice. If we do not have a single-cell RNA-seq reference dataset for slice information specifically. How to do this experiment in other methods for benchmarking? Thanks in advance!

Best regards, Cristal