How rto download single cell RNAseq data in patchseq

Hi Allen Community,

I am trying to learn patch-seq data on your website, and I want to download patch-seq data for analysis. But I find the single-cell RNAseq data you put on NEMO is under control. How can I get access to obtain single-cell RNAseq data of patch-seq?

I know maybe I have to do some paperwork, may you let me know how to send my application

Thank you so much,


Hi Heather, can you direct me to where are you are trying to download the data from? I need to know what source/link you are accessing before I can answer.

That is my fault. I want to download patch-seq data from your website on there url for data. I found that your patch-seq data are stored separately, so I click the red box on this picture to download RNAseq data

I turn to the NEMO website, and I could not find the Source Data URL like the picture below

There is the URL for data stored in NEMO RNAseq_data_stored_in_NEMO_url



Thanks Heather. On those links there should be a link /explanation on how to complete our NDA to gain access to our data. We are reaching out to our NeMO folks to restore this and I will contact you as soon as it is complete.

Thank you so much, Brian Lee, for helping me with the download link! Your assistance is greatly appreciated!

Hi Heather, here is the link to complete the NDA - this is required to access our data. This should be on the page you accessed and NeMO is currently working to make it more accessible. NeMO Archive - Accessing Controlled Access Data

Hi, Lee.

Thanks for your help! I really appreciate it. But now, it says my account doesn’t affiliate with the NIH-Recognized Research Institution. Is there any way I can do to deal with it? How can my account get permission from the institution? Should I sign a new account for it? If not, can I download these data from other websites?


Hi Heather, accounts must be set up using an institutional email address.

Looks to me like the dataset link is now available at the NEMO landing page (NeMO Data Archive Assets), with a direct link to Index of /other/AIBS/AIBS_patchseq/transcriptome/scell/SMARTseq. This shouldn’t be controlled access data, @brian_lee maybe you were mixing this up with the human cell data?