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Series GSE126310 Query DataSets for GSE126310
Status Public on Mar 01, 2019
Title Expanding the CITE-seq tool-kit: Detection of proteins, transcriptomes, clonotypes and CRISPR perturbations with multiplexing, in a single assay
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Multi-modal single-cell assays provide high-resolution snapshots of complex cell populations but are mostly limited to transcriptome plus an additional modality. Here, we describe Expanded CRISPR-compatible Cellular Indexing of Transcriptomes and Epitopes by sequencing (ECCITE-seq) for the high-throughput characterization of at least five modalities of information from each single cell. We demonstrate application of ECCITE-seq to multimodal CRISPR screens with robust direct sgRNA capture and to clonotype-aware multimodal phenotyping of cancer samples.
Overall design All experiments were performed using the 10x genomics V(D)J solution which incorporates scRNA-seq with additional profiling of protein surface markers and sgRNAs (when present). Antibody oligo counts are listed in the ADT and HTO tables and sgRNAs counts in the GDO tables.

>>>The raw data for the samples GSM3596095, GSM3596098, GSM3596099, GSM3596100, GSM3596103, and GSM3596104 are being submitted to dbGaP due to patient privacy concerns<<<
Contributor(s) Mimitou E, Smibert P
Citation(s) 31011186, 31465740
Submission date Feb 08, 2019
Last update date Oct 05, 2020
Contact name Eleni Mimitou
Organization name New York Genome Center
Lab Technology Innovation Lab
Street address 101 Avenue of the Americas
City New York
State/province NY
ZIP/Postal code 10013
Country USA
Platforms (3)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL22245 Illumina HiSeq 2500 (Homo sapiens; Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (24)
GSM3596081 sp-cDNA
GSM3596082 sp-ADT
GSM3596083 sp-GDO
BioProject PRJNA521522
SRA SRP184710

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE126310_RAW.tar 125.3 Mb (http)(custom) TAR (of CSV, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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