Please help with the scRNA-seq labels?

[bitcometz]

hello, thanks for this great tool!

I downloaded the big file sagenet_paper.tar.gz.

The original labels for scRNA-seq data is "Forebrain/Midbrain/Hindbrain".

Could you tell me where I can got the separated labels "Forebrain", "Midbrain", "Hindbrain" for each cells in the scRNA-Seq dataset?

Best, Jinbo

[shazanfar]

Hi Jinbo,

Thanks for this! This dropbox link is for an RDS file containing a named character vector of the specific "Forebain/Midbrain/Hindbrain" labels https://www.dropbox.com/scl/fi/2pzvt9q2urhxw6v5xxu1y/E8.5_brain_cluster.Rds?rlkey=32rh6npdp237tkgj2ss3rryya&dl=0

Note they are at a higher resolution with the following mapping: Telencephalon = forebrain Mesencephalon = midbrain Rhombencephalon = hindbrain

Hope that helps!

Best wishes, Shila

[bitcometz]

Dear shila @shazanfar , Thanks for your help ! I download the data and output as :

"embryo1_Pos1_cell32_z2"        "Prosencephalon 1"
"embryo1_Pos1_cell32_z5"        "Mesencephalon"
"embryo1_Pos1_cell33_z2"        "Mesencephalon"
"embryo1_Pos1_cell33_z5"        "Mesencephalon"

But I don't know how to match up the two files by cell ID; it seems like they're not from the same dataset.

adata = sc.read_h5ad("/path/Lohoff/adata_scRNAseq.h5ad")
adata.obs.head(10)

Besides, I like this software. And I am doing to build SageNet results on the streamlit share cloud. So every one can know its results. I am still working on this: https://sgr-sagenet.streamlit.app/

Best, Jinbo

[shazanfar]

Hi Jinbo, Thank you for your interest! You are correct, the labels I sent you are the additional subset labels for the seqFISH spatial data, starting like "embryo1_Pos1_cell32_z2". The cells that are labelled similar to "cell_36866" are belonging to the scRNA-seq reference used in the integration (Pijuan-Sala et al Nature 2019), and do not have any spatial component. The scRNA-seq dataset can be accessed via Bioconductor MouseGastulationData package, or directly through the publication data availability page. I hope that helps! Best wishes, Shila