GEO series

Cryopreservation of cerebrospinal fluid cells preserves transcriptomics integrity for single-cell analysis

GSE252701 Homo sapiens (human) Single-cell RNA-seq 35 samples Submitted 2024/03/26 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 35 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: 35 samples: 28 distinct titles, 5 of them repeatedGroups 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.
Paper: Cryopreservation of cerebrospinal fluid cells preserves the transcriptional landscape for single-cell analysisJournal of neuroinflammation · 2024

Summary (written by the submitters)

Cerebrospinal fluid (CSF) matrix biomarkers have become increasingly valuable surrogate markers of neuropsychiatric diseases in research and clinical practice. In contrast, CSF cells have been rarely investigated due to their relative scarcity and fragility, and lack of common collection and cryopreservation protocols, with limited exceptions for neurooncology and primary immune-based diseases like multiple sclerosis.

Read the full summary ↓

The advent of a microfluidics-based multi-omics approaches to studying individual cells has allowed for the study of cellular phenotyping, intracellular dynamics, and intercellular relationships that provide multidimensionality unable to be obtained through acellular fluid-phase analyses. challenges to cell-based research include site to- site differences in handling, storage, and thawing methods, which can lead to inaccuracy and inter-assay variability. In the present study, we performed single-cell RNA sequencing (10x Genomics) on fresh (Samples labeled as FRE) or previously cryopreserved human CSF samples from three alternative cryopreservation methods: Fetal Bovine Serum with Dimethyl sulfoxide (FBS/DMSO, Samples labeled as FBS), FBS/DMSO after a DNase step (a step often included in epigenetic studies, samples labeled as DNA), and cryopreservation using commercially available Recovery©media (Samples labeled as REC). In comparing relative differences between fresh and cryopreserved samples, we found little effect of the cryopreservation method on being able to resolve donor-linked cell type proportions, markers of cellular stress, and overall gene expression at the single-cell level, whereas donor-specific differences were readily discernable. We further, demonstrate the compatibility of fresh and cryopreserved CSF immune cell sequencing using biologically relevant sexually dimorphic gene expression differences by donor. Our findings support the utility and interchangeability of FBS/DMSO and Recovery cryopreservation with fresh sample analysis, providing a methodological grounding that will enable researchers to further expand our understanding of the CSF immune cell contributions to neurological and psychiatric disease.

Published in

Cryopreservation of cerebrospinal fluid cells preserves the transcriptional landscape for single-cell analysis

Kodali MC, Antone J, Alsop E et al. · Journal of neuroinflammation 2024 · PMID 38521932 · doi:10.1186/s12974-024-03047-1

This dataset

Open GSE252701 in finder → Find more human 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 GSE252701_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 PRJNA1062285 and SRA study SRP482409. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38521932) ↗

Study design

28 distinct titles, 5 of them repeated

Sample_A_FRE ×3 Sample_I_FBS ×3 Sample_A_DNA ×2 Sample_A_FBS ×2 Sample_A_REC ×2

How we read this: Read from 35 sample titles: 28 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

GSM8005382 Sample_A_DNA_1
GSM8005383 Sample_A_DNA_2
GSM8005384 Sample_A_FBS_1
GSM8005385 Sample_A_FBS_2
GSM8005386 Sample_A_FRE_1
GSM8005387 Sample_A_FRE_2
GSM8005388 Sample_A_FRE_3
GSM8005389 Sample_A_REC_1
GSM8005390 Sample_A_REC_2
GSM8005391 Sample_B_FBS
GSM8005392 Sample_B_FRE
GSM8005393 Sample_B_REC
GSM8005394 Sample_C_DNA
GSM8005395 Sample_C_FBS
GSM8005396 Sample_C_FRE
GSM8005397 Sample_C_REC
GSM8005398 Sample_D_DNA
GSM8005399 Sample_D_FBS
GSM8005400 Sample_D_REC
GSM8005401 Sample_E_FBS
GSM8005402 Sample_E_FRE
GSM8005403 Sample_E_REC
GSM8005404 Sample_F_DNA
GSM8005405 Sample_F_FBS
GSM8005406 Sample_F_REC
GSM8005407 Sample_G_DNA
GSM8005408 Sample_G_FBS
GSM8005409 Sample_G_REC
GSM8005410 Sample_H_FRE
GSM8005411 Sample_H_REC
GSM8005412 Sample_I_FBS_1
GSM8005413 Sample_I_FBS_2
GSM8005414 Sample_I_FBS_3
GSM8005415 Sample_J_FBS
GSM8005416 Sample_J_FRE

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