GEO series

Massively multiplex multi-modal chemical screens at single-cell resolution with icCITE-plex

GSE300551 Homo sapiens (human) Single-cell RNA-seq 25 samples Submitted 2026/04/14 Platform GPL25526

At a glance

Single-cell RNA-seq · human · 25 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 25 samples: 25 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

We present icCITE-plex, a novel cellular barcoding systems that enable multiplexed analysis of multiple independent samples within a single experiment through a combination of viral barcodes and antibody-based plate-barcodes. Using this platform, we successfully profiled 360 drug-dose responses across 475 surface proteins, 64 intracellular epitopes, and the whole transcriptome in human and mouse T cells treated with 56 different kinase inhibitors, demonstrating the method's ability to capture multi-modal cellular responses to chemical perturbations.

This dataset

Open GSE300551 in finder → Find more RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE300551_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1281163 and SRA study SRP593995. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

25 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 25 sample titles: 25 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM9064445 icCITE-seq RNA library D9
GSM9064446 icCITE-seq RNA library E9
GSM9064447 icCITE-seq RNA library F9
GSM9064448 icCITE-seq RNA library G9
GSM9064449 icCITE-seq RNA library H9
GSM9064450 icCITE-seq ADT library D9
GSM9064451 icCITE-seq ADT library E9
GSM9064452 icCITE-seq ADT library F9
GSM9064453 icCITE-seq ADT library G9
GSM9064454 icCITE-seq ADT library H9
GSM9064455 icCITE-seq HTO library D9
GSM9064456 icCITE-seq HTO library E9
GSM9064457 icCITE-seq HTO library F9
GSM9064458 icCITE-seq HTO library G9
GSM9064459 icCITE-seq HTO library H9
GSM9064460 icCITE-seq TSB library D9
GSM9064461 icCITE-seq TSB library E9
GSM9064462 icCITE-seq TSB library F9
GSM9064463 icCITE-seq TSB library G9
GSM9064464 icCITE-seq TSB library H9
GSM9064465 icCITE-seq CT library D9
GSM9064466 icCITE-seq CT library E9
GSM9064467 icCITE-seq CT library F9
GSM9064468 icCITE-seq CT library G9
GSM9064469 icCITE-seq CT library H9

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.