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YangLabHKUST / STitch3D

Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices
https://stitch3d-tutorial.readthedocs.io/en/latest/index.html#
MIT License
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Where can I find the single cell RNAseq count data for each slice? #21

Open cristalliao opened 1 year ago

cristalliao commented 1 year ago

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:

Screen Shot 2023-08-13 at 2 58 28 pm Screen Shot 2023-08-13 at 2 58 18 pm

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:

Screen Shot 2023-08-13 at 3 00 54 pm Screen Shot 2023-08-13 at 3 01 05 pm

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 commented 1 year ago

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 commented 1 year ago

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