Data acquisition issue

[YuzhiSun]

Hi @bnprks , Thank you very much for your contribution to multi omics sequencing data, I would like to ask you a question on how to quickly obtain the three omics data matrices you measured. I would like to use the three omics matrices for downstream analysis.

Best regards, Yuzhi

[bnprks]

Hi Yuzhi,

The data for this paper is deposited on GEO, at this link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178707

If you hit (custom) under the download link, then you can select a subset of the files you want to download. Assuming you're interested in the T cell data matrices, I think the files you would want are:

• GSM5396333_lane1* - files for a 10x text-based feature matrix for lane 1 cells. This contains both RNA and ATAC information, but I'd recommend just keeping the RNA part since the ATAC peak calls might not line up with lane 2
• GSM5396337_lane2* - equivalent for lane 2 cells
• GSM*_ADT_counts_lane*.csv.gz - TF ADT read counts for each lane
• GSM*_HTO_counts_lane*.csv.gz - Hashing ADT read counts for each lane (we used for some normalization)
• GSM5396336_CD4_Peak_matrix.rds.gz - The peak matrix from our analysis combining lanes 1 + 2, where each barcode has lane1# or lane2# prepended to it

There are several other files available from GEO, and if you want to replicate something specifically from the paper a lot of our scripts are present in this repo. Our code_utils/download_data.py file will download all the raw data you need, but it may be more than you want for your specific use-case.

Hope that helps!

-Ben