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lawrenson-lab / AtlasEndometriosis

A single-cell transcriptomic analysis of endometriosis, endometriomas, eutopic endometrial samples and uninvolved ovary tissues highlights cell populations characteristic of these tissue types. Transcriptional and cellular heterogeneity across tissues suggests novel therapeutic targets and biomarkers for this disease.
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Request for Loupe files #1

Open marswh12312313 opened 7 months ago

marswh12312313 commented 7 months ago

I am currently conducting a research project on endometriosis, and the spatial transcriptomic data presented in your article would be invaluable for my study. I was wondering if you would be willing to share the Loupe files from your analysis. Having access to these files would greatly enhance my understanding of your analytical processes and results, which would be incredibly helpful for my own research.

I assure you that the data will be kept strictly confidential and will only be used for research purposes. I will also make sure to properly cite your work in any resulting publications.

I would be immensely grateful if you could take the time to consider my request. If you are willing to share the data, please let me know, and I will promptly respond with details on how to securely transfer the files.

Thank you for your time and attention. I sincerely appreciate the significant contributions you and your team have made to the field of endometriosis research.

Best regards

marswh12312313 commented 7 months ago

I found it hard to use the spatial data in GEO. I will glad if you share the Loupe files :）

mabraao commented 7 months ago

Hello, thanks for you message and your interest in analysing the data. Unfortunetly I dont have the loupe files. Do you think it works to generate a seurat object and then convert it tp Loupe file? Here I have some procedures:

Load a 10x Genomics Visium Spatial Experiment into a Seurat object https://satijalab.org/seurat/reference/load10x_spatial

LoupeR to Generate CLOUPE files from Seurat Objects https://www.10xgenomics.com/support/software/loupe-browser/latest/tutorials/introduction/lb-louper

Thanks!

marswh12312313 commented 7 months ago

Seurat expects input in .h5 format, but your GEO series only provides unfiltered .mtx, making it difficult for me to use. I know this might be bothersome, but I would be immensely grateful if you could provide the original Seurat .rds format object or a standard h5 format file for generate a Seurat object.