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mafeiyang / leprosy_amg_network

Single Cell and Spatial Transcriptomics Defines the Cellular Architecture of the Antimicrobial Response Network in Human Leprosy Granulomas
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Coordinates of spots for files deposited on GEO #1

Open gokceneraslan opened 2 years ago

gokceneraslan commented 2 years ago

Hi,

I am trying to load the spatial transcriptomics data that are deposited on GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5115019) but as far as I see, the files mapping the barcodes to the tissue coordinates are missing. Is that right? Using the files on GEO, I am able to work with the count matrix and I can see the tissue hires PNG file but there is nothing about the coordinates, so I am not able to use the "spatial" info of the spatial data basically.

I am aware of the R files on gdrive (https://drive.google.com/drive/folders/10rnX0DHHvukS3evpw9zE9TrycusBtNoT) but I was wondering if the raw files for all 6 slides are available, so that I can use my own pipeline (i.e. SquidPy) for the analysis.

Thanks, Gokcen.

gokceneraslan commented 2 years ago

I think the missing files are "tissue_positions_list.csv" and "scalefactors_json.json". It'd be great to have these files for all 6 slides. See this GEO record for another Visium upload with coordinates:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4565826