Question

Finding scRNA-seq datasets of healthy human ovaries

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5 months ago

JACKY ▴ 160

I am searching for scRNA-seq data of healthy human ovaries (or healthy fallopian tubes).

I have searched in GEO, ArrayExpress , and Google Scholar, still I only found two suitable datasets, I need at least two more and it seems there is none!

Can anyone here help me please ? I am looking for unsorted data, counts (important to be unnormalized), and rich with as much cells as possible from all kinds!

Needless to say, the higher the number of patients / samples in a dataset, the better. And it's important that it's just a normal healthy tissue and not from inflamed or cancerous ovaries..

Thanks!

python GEO single-cell RNA • 696 views

ADD COMMENT • link updated 5 months ago by Ram 44k • written 5 months ago by JACKY ▴ 160

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https://explore.data.humancellatlas.org/projects/faeedcb0-e046-4be7-b1ad-80a3eeabb066

https://explore.data.humancellatlas.org/projects/0d4aaaac-02c3-44c4-8ae0-4465f97f83ed

https://explore.data.humancellatlas.org/projects/2b81ecc4-6ee0-438f-8c5b-c10b2464069e

ADD REPLY • link 5 months ago by GenoMax 147k

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I'll comment regarding each one of these:

1) I've seen this, they have this weird source of samples (taken from stroma and follicles of ovaries) which I didn't fully get. I wasn't sure I can use this cause stroma samples won't have a diverse types of cells

2) These are snRNA-seq and snATAC-seq. I need scRNA-seq

3) Again, no ovarian scRNA-seq

ADD REPLY • link 5 months ago by JACKY ▴ 160

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On the one hand, your request is genuinely good - resources ought to be findable and samples sequenced once should be available for everyone to use. But on the other hand, who would fund single cell analyses of healthy tissue alone? If you're answering a biological question of interest that needs such specific tissue, maybe you are the one that will end up providing this resource/pioneering this project.

ADD REPLY • link 5 months ago by Ram 44k

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You bring a valid point, but still there must be more sequencing data for healthy tissues somewhere, I don't believe that just two random datasets have done such sequencing and that's it.

Also, if you're familiar with datasets that have both Healthy and Cancerous samples (such as GSE184880), that is also ok, I'll just use the healthy samples.

ADD REPLY • link 5 months ago by JACKY ▴ 160

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I'm not familiar with ovarian cancer datasets (I am currently working on a few ovarian cancer datasets but none of them are healthy/normal samples). I do think you'll have better luck looking at ovarian cancer samples with matched normals. TCGA might be of use there.