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Series GSE135325 Query DataSets for GSE135325
Status Public on Mar 30, 2020
Title A targeted multi-omic analysis approach measures protein expression and low abundance transcripts on the single cell level
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary High throughput single-cell RNA sequencing (sc-RNAseq) has become a frequently used tool to assess immune cell function and heterogeneity. Recently, the combined measurement of RNA and protein expression by sequencing was developed, which is commonly known as CITE-Seq. Acquisition of protein expression data along with transcriptome data resolves some of the limitations inherent to only assessing transcript, but also nearly doubles the sequencing read depth required per single cell. Furthermore, there is still a paucity of analysis tools to visualize combined transcript-protein datasets.
Here, we describe a novel targeted transcriptomics approach that combines analysis of over 400 genes with simultaneous measurement of over 40 proteins on more than 25,000 cells. This targeted approach requires only about 1/10 of the read depth compared to a whole transcriptome approach while retaining high sensitivity for low abundance transcripts. To analyze these multi-omic transcript-protein datasets, we adapted One-SENSE for intuitive visualization of the relationship of proteins and transcripts on a single-cell level.
Overall design Immune cell characterization utilizing targeted single cell RNA sequencing paired with oligo tagged antibodies using the BD Rhapsody/ AbSeq system
Contributor(s) Prlic M, Erickson JR, Mair F
Citation(s) 32268080
Submission date Aug 02, 2019
Last update date May 19, 2020
Contact name Martin Prlic
Phone 2066672216
Organization name Fred Hutch
Street address 1100 Fairview Ave, Mail stop E5-110
City Seattle
State/province WA
ZIP/Postal code 98108
Country USA
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (6)
GSM4005486 PBMC AbSeq_1
GSM4005487 PBMC AbSeq_2
GSM4005488 SubSample
BioProject PRJNA558392

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
GSE135325_AbSeq_38plex.fasta.gz 989 b (ftp)(http) FASTA
GSE135325_AbSeq_41plex.fasta.gz 1004 b (ftp)(http) FASTA
GSE135325_AbSeq_Stim.fasta.gz 511 b (ftp)(http) FASTA
GSE135325_BD_Rhapsody_T_Cell_Expression_Panel_Hs.fasta.gz 29.8 Kb (ftp)(http) FASTA
GSE135325_Donor_3_SampleSheet.csv.gz 101 b (ftp)(http) CSV
GSE135325_PBMC_Rhapsody_amplicons.fasta.gz 59.3 Kb (ftp)(http) FASTA
GSE135325_RAW.tar 14.7 Mb (http)(custom) TAR (of CSV, MTX, TSV)
Raw data are available in SRA
Processed data provided as supplementary file

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