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Systematic Bias Introduced by Ficoll-Based Isolation in AML Sample Composition and Downstream Analyses

GSE313042 Homo sapiens (human) RNA-seq (gene expression) 10 samples Submitted 2025/12/16 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 10 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Topic
Acute myeloid leukemiaThis series is part of our curated briefing on it.
Samples
10 samples: 5 × Leukocytes_Lysis_P vs 5 × Leukocytes_Ficoll_PGroups 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)
Acute myeloid leukemia (AML) is a heterogeneous malignancy whose characterization relies on immunophenotyping and molecular profiling. While red blood cell lysis is the recommended method for leukocyte isolation in clinical diagnostics, Ficoll-based density gradient centrifugation remains widely used in research and biobanking. Here, we systematically compare these two isolation approaches using paired primary AML samples.
Read the full summary ↓
We show that Ficoll processing consistently enriches lymphocytes and AML blasts while depleting granulocytes. The increased T-cell content introduced by Ficoll impaired AML engraftment in immunodeficient NSG mice, as residual T cells in the graft triggered graft-versus-host disease, precluding reliable evaluation of leukemia-initiating activity. Although Ficoll had minimal impact on ex-vivo AML blast expansion or chemotherapy response, RNA sequencing identified 1,136 differentially expressed genes between isolation methods, with Ficoll samples exhibiting enrichment of proliferation-associated pathways and leukemic stem cell (LSC) transcriptional programs. Immunogenomic deconvolution further demonstrated that Ficoll artificially inflates estimated CD8⁺ T-cell and monocyte abundances while reducing inferred neutrophil frequencies. Mutation calling from RNA-seq data revealed substantial discrepancies between methods, including failure to detect a clinically relevant DNMT3A R882 mutation in a Ficoll-processed sample. These findings identify leukocyte isolation as a critical pre-analytical variable in AML research and support the systematic use of red blood cell lysis to preserve cellular diversity and avoid unpredictable biases introduced by Ficoll-based isolation.
This dataset
Open GSE313042 in finder → Find more human RNA-seq datasets → Acute myeloid leukemia landscape →
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 GSE313042_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1378179 and SRA study SRP653775. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 × Leukocytes_Lysis_P vs 5 × Leukocytes_Ficoll_P

Supports a between-group comparison across 10 samples.

How we read this: 2 replicated groups read from 10 sample titles; they account for 10 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
More Acute myeloid leukemia datasets

Search all human RNA-seq datasets in GEO →

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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.