Reads-per-UMI tables across single-cell RNA sequencing protocols

Data analyzed in Lause, Ziegenhain et al. (2023).

Code to obtain these tables from public data sources is available on github.

Each row in the table is a UMI-tag detected in a certain cell (column RG) attached to a molecule from a specific gene (column GE) with a certain barcode (column UB). Column N gives the number of times the UMI was detected for that gene and cell.

Data sources and protocols are given with the respective file names below.

Johnsson2022_Smartseq3_PE.hd1.txt.gz: Mouse fibroblasts profiled with Smart-seq3 paired-end; accession E-MTAB-10148, sample plate2,
Paper

Hagemann-Jensen2020_Smartseq3_SE.hd1.txt.gz: Mouse fibroblasts profiled with Smart-seq3 single-end; accession E-MTAB-8735, sample Smartseq3.Fibroblasts.smFISH
Paper

Hagemann-Jensen2022_Smartseq3xpress.hd1.txt.gz: HEK293 cells profiled with Smart-seq3Xpress; accession E-MTAB-11467.
Paper

Ziegenhain2017.hd1.txt.gz: Mouse embryonic stem cells profiled by CEL-seq2, Drop-seq, MARS-seq, and SCRB-seq; GEO accession GSE75790
Paper