GEO series

Split-pool combinatorial barcoding sequencing of murine immune cells

GSE253406 Mus musculus (mouse) Single-cell RNA-seq 13 samples Submitted 2024/10/23 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 13 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 13 samples: 9 × Parse WT, sublibrary vs 2 × Parse Mini, sublibraryGroups 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)

Single-cell RNA sequencing experiments commonly use 10x Genomics kits due to their high-throughput capacity and standardized protocols. Recently, Parse Biosciences introduced an alternative technology that uses multiple in-situ barcoding rounds within standard 96-well plates. The Parse technology allows the analysis of more cells from multiple samples in a single run without using additional reagents or specialized microfluidics equipment.

Read the full summary ↓

To assess the efficacy of both platforms, we carried out a benchmark study using biological and technical replicates of young murine thymus as a complex immune tissue. To optimally utilize the capacity of Parse high-throughput kits, we also performed sequencing of murine splenocytes from a chronic stress model and control animals.

This dataset

Open GSE253406 in finder → Find more mouse 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 GSE253406_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 PRJNA1065472 and SRA study SRP484103. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

9 × Parse WT, sublibrary vs 2 × Parse Mini, sublibrary

Supports a between-group comparison across 11 samples.

How we read this: 2 replicated groups read from 13 sample titles; they account for 11 of them. 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

GSM8020231 Parse WT, sublibrary 1 Parse WT, sublibrary
GSM8020232 Parse WT, sublibrary 2 Parse WT, sublibrary
GSM8020233 Parse WT, sublibrary 3 Parse WT, sublibrary
GSM8020234 Parse WT, sublibrary 4 Parse WT, sublibrary
GSM8020235 Parse WT, sublibrary 5 Parse WT, sublibrary
GSM8020236 Parse WT, sublibrary 6 Parse WT, sublibrary
GSM8020237 Parse WT, sublibrary 7 Parse WT, sublibrary
GSM8020238 Parse WT, sublibrary 8 Parse WT, sublibrary
GSM8020239 Parse WT, sublibrary 9 Parse WT, sublibrary
GSM8020240 Parse Mini, sublibrary 1 Parse Mini, sublibrary
GSM8020241 Parse Mini, sublibrary 2 Parse Mini, sublibrary
GSM8020242 10x Genomics, Gene Expression
GSM8020243 10x Genomics, Hashtags

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Search all mouse RNA-seq datasets in GEO →

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