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Series GSE163089 Query DataSets for GSE163089
Status Public on Dec 13, 2020
Title Tailoring the resolution of single-cell RNA sequencing for primary cytotoxic T cells
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Single-cell RNA sequencing in principle offers unique opportunities to improve the efficacy of contemporary T-cell based immunotherapy against cancer. The use of high-quality single-cell data will aid our incomplete understanding of molecular programs determining the differentiation and functional heterogeneity of cytotoxic T lymphocytes (CTLs) allowing for optimal therapeutic design. So far a major obstacle to high depth single-cell analysis of CTLs is the minute amount of RNA available leading to low capturing efficacy. To overcome this we tailor a droplet-based approach for high-throughput analysis (tDrop-seq) and a plate-based method for high-performance in-depth CTL analysis (tSCRB-seq). The latter gives on average a 15-fold higher number of captured transcripts per gene compared to droplet-based technologies. The improved dynamic range of gene detection gives tSCRB-seq an edge in resolution sensitive downstream applications such as graded high confidence gene expression measurements and cluster characterization. We demonstrate the power of tSCRB-seq by revealing the subpopulation-specific expression of co-inhibitory and co-stimulatory receptor targets of key importance for immunotherapy.
Overall design This study groups a total of 27 samples of single-cell RNA sequencing with two different protocols (Drop-seq and SCRB-seq) and their modifications.
Contributor(s) Kanev K, Roelli P, Wu M, Wurmser C, Delorenzi M, Pfaffl MW, Zehn D
Citation(s) 33495472
Submission date Dec 12, 2020
Last update date Feb 02, 2021
Contact name Patrick Roelli
Organization name TUM
Department Tierphysiologie & Immunologie
Lab Dr. Zehn
Street address Weihenstephaner Berg 3
City Freising
ZIP/Postal code 85354
Country Germany
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL22245 Illumina HiSeq 2500 (Homo sapiens; Mus musculus)
Samples (27)
GSM4971874 DS_mix_HS/MM_D0_ctrl_1
GSM4971875 DS_mix_HS/MM_D0_ctrl_2
GSM4971876 DS_mix_HS/MM_D0_ctrl_3
BioProject PRJNA684762
SRA SRP297763

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE163089_DS_config.yaml.txt.gz 648 b (ftp)(http) TXT
GSE163089_SCRB_barcodes.csv.gz 283 b (ftp)(http) CSV
GSE163089_SCRB_config.yaml.txt.gz 678 b (ftp)(http) TXT
GSE163089_barcodes.tsv.gz 10.7 Kb (ftp)(http) TSV
GSE163089_custom_adapters.fa.gz 225 b (ftp)(http) FA
GSE163089_features.tsv.gz 175.8 Kb (ftp)(http) TSV
GSE163089_gtf_biotypes.yaml.txt.gz 314 b (ftp)(http) TXT
GSE163089_matrix.mtx.gz 7.5 Mb (ftp)(http) MTX
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Raw data are available in SRA
Processed data are available on Series record

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