GSE241238

PBMCs from healthy volunteers or septic patients

Whole-study status Exploratory only

Dataset can inform exploration but is not strong enough for primary analysis.

Whole-study downloads — these do not apply your sample requirements.

Selected cohort requirements

Samples meeting selected requirements: 0 cases / 0 controls

View matching samples

Patient pairs verified in indexed sample metadata: 0

A case/control comparison meeting these requirements is not confirmed.

Counts describe samples, not independent patients. Pair verification uses explicit subject identifiers in indexed sample metadata. Zero verified pairs does not establish that the study is unpaired; reported matched-normal design alone is insufficient.

Source: GEO
Assay: bulk RNA-seq
Organism: Homo sapiens
Whole-study samples: 8 samples
Specimen: Biofluid
Reported/interpreted study design: Patient biofluid vs healthy control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Qiao Z
Contact name: zigang qiao
Submission date: 2023-08-18
Last update: 2024-08-15
Organization: Chinese Academy of MedicalSciences & Peking Union Medical College
Department: Suzhou Institute of Systems Medicine
Public date: 2024-08-15
Experiment types: Expression profiling by high throughput sequencing
Platforms: GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Series type: Series
SubSeries: Not available
BioProject: PRJNA1006774

Summary

This study aimed to analyze and compare the test transcripts of peripheral blood mononuclear cells (PBMCs) isolated from 4 healthy donors and 4 septic patients' whole blood.

Overall design

Gene expression profiling analysis of RNA-seq data for PBMCs from healthy volunteers or septic patients

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 8 GSM samples	Primary source
recount3	Planned trusted source for processed count availability.	No match found
Expression Atlas	Planned source for curated expression experiment links.	No match found
PubMed	Primary GEO citations and related PubMed articles that mention this dataset. 1 linked publication 1 DOI Related publications LncRNA TUG1 mitigates sepsis-induced acute lung injury via a ceRNA network regulating the CALM1/PRKG1/RYR3/AQP5 axis. Scientific reports, 2026 PubMed DOI	Available

Metadata Quality Components

Persisted metadata quality

100 pts

Clarity: 100%
Weight: 100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Anatomical source metadata normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Analysis Readiness

Ready after review

100% DE readiness

Contrast completeness

25/25 pts

Both case and control groups are present in the proposed grouping.

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

15/15 pts

All samples are assigned to a case or control group.

Blocking warnings

10/10 pts

No dataset warnings are present.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

No readiness blockers detected.

Next Steps

Verify the proposed sample assignments and case-versus-control comparison against the GEO metadata before using them in DESeq2 or another differential-expression tool.
Confirm processed count files and sample identifiers match the exported metadata.

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

Siftome proposed case and control labels, but no reviewer confirmation is stored yet.

Open the sample grouping CSV and confirm group labels before analysis.

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

Confirm whether the cohort is large enough for the intended statistical analysis.

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

Verify that downloaded processed files contain usable count or expression identifiers.

Ambiguous samples handled

Ready

No review-needed or unassigned samples are present in the proposed grouping.

Review the grouping table for biologically meaningful differences that the automated checks may not detect.

Exclusion decisions recorded

Ready

No hard-excluded samples were detected by the current rules.

Record any manual exclusions in the downstream analysis notes.

Source traceability preserved

Ready

The dataset and sample accessions can be traced back to GEO.

Keep GEO accessions with exported metadata.

Bioinformatician Review

Standard analyst review

Proceed only after the analyst confirms grouping, exclusions, and source files.

By Siftome standards, no expert review was triggered.

Why This Is Ranked Here

Tumor vs normal

Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.

Applied Review Decisions

No active review decisions affect this ranking.

Derived Classifications

Disease context Sepsis Disease context came from Normalization rules.
Likely case group Sepsis or systemic inflammatory response 4 samples
Likely control group Healthy control 4 samples

Intent Interpretation

Downgrade or exclusion reason Downgraded for tissue search because it is a biofluid cohort. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 10%.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Sepsis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 42143071.
Publication context: LncRNA TUG1 mitigates sepsis-induced acute lung injury via a ceRNA network regulating the CALM1/PRKG1/RYR3/AQP5 axis.. Scientific reports, 2026. PMID 42143071. DOI 10.1038/s41598-026-51003-1.

Cautions

Downgraded for tissue search because it is a biofluid cohort.
Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
Overall score capped because comparison suitability is weak for the selected search intent.
Overall score capped because fewer than ten samples limit cohort confidence.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

No dataset warnings

Normalized Fields

40 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source blood GSM7719862 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmcs source_name: PBMCs sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7719863 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmcs source_name: PBMCs sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7719864 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmcs source_name: PBMCs sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7719865 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmcs source_name: PBMCs sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7719866 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmcs source_name: PBMCs sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7719867 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmcs source_name: PBMCs sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7719868 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmcs source_name: PBMCs sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM7719869 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmcs source_name: PBMCs sample-anatomical-source-v1 sample-local anatomical source

assay_type bulk RNA-seq GSE241238 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence bulk rna-seq dataset_accession: GSE241238 dataset_title: PBMCs from healthy volunteers or septic patients organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true raw_d... keyword match keyword match: bulk rna-seq

cell_population peripheral blood mononuclear cells GSM7719862 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs PBMCs, Healthy-1 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Healthy controlled vocabulary controlled vocabulary cell population match: pbmcs

cell_population peripheral blood mononuclear cells GSM7719863 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs PBMCs, Healthy-2 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Healthy controlled vocabulary controlled vocabulary cell population match: pbmcs

cell_population peripheral blood mononuclear cells GSM7719864 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs PBMCs, Healthy-3 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Healthy controlled vocabulary controlled vocabulary cell population match: pbmcs

cell_population peripheral blood mononuclear cells GSM7719865 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs PBMCs, Healthy-4 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Healthy controlled vocabulary controlled vocabulary cell population match: pbmcs

cell_population peripheral blood mononuclear cells GSM7719866 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs PBMCs, Sepsis-1 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Sepsis controlled vocabulary controlled vocabulary cell population match: pbmcs

cell_population peripheral blood mononuclear cells GSM7719867 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs PBMCs, Sepsis-2 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Sepsis controlled vocabulary controlled vocabulary cell population match: pbmcs

cell_population peripheral blood mononuclear cells GSM7719868 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs PBMCs, Sepsis-3 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Sepsis controlled vocabulary controlled vocabulary cell population match: pbmcs

cell_population peripheral blood mononuclear cells GSM7719869 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs PBMCs, Sepsis-4 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Sepsis controlled vocabulary controlled vocabulary cell population match: pbmcs

disease sepsis GSE241238 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence septic patients dataset_accession: GSE241238 dataset_title: PBMCs from healthy volunteers or septic patients organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true raw_d... controlled vocabulary controlled vocabulary disease match: septic patients

disease sepsis GSM7719866 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence sepsis PBMCs, Sepsis-1 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Sepsis controlled vocabulary controlled vocabulary disease match: sepsis

disease sepsis GSM7719867 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence sepsis PBMCs, Sepsis-2 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Sepsis controlled vocabulary controlled vocabulary disease match: sepsis

disease sepsis GSM7719868 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence sepsis PBMCs, Sepsis-3 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Sepsis controlled vocabulary controlled vocabulary disease match: sepsis

disease sepsis GSM7719869 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence sepsis PBMCs, Sepsis-4 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Sepsis controlled vocabulary controlled vocabulary disease match: sepsis

organism Homo sapiens GSE241238 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE241238 dataset_title: PBMCs from healthy volunteers or septic patients organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true raw_d... keyword match keyword match: homo sapiens

specimen_material PBMC preparation GSM7719862 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs PBMCs, Healthy-1 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Healthy controlled vocabulary controlled vocabulary specimen material match: pbmcs

specimen_material PBMC preparation GSM7719863 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs PBMCs, Healthy-2 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Healthy controlled vocabulary controlled vocabulary specimen material match: pbmcs

specimen_material PBMC preparation GSM7719864 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs PBMCs, Healthy-3 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Healthy controlled vocabulary controlled vocabulary specimen material match: pbmcs

specimen_material PBMC preparation GSM7719865 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs PBMCs, Healthy-4 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Healthy controlled vocabulary controlled vocabulary specimen material match: pbmcs

specimen_material PBMC preparation GSM7719866 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs PBMCs, Sepsis-1 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Sepsis controlled vocabulary controlled vocabulary specimen material match: pbmcs

specimen_material PBMC preparation GSM7719867 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs PBMCs, Sepsis-2 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Sepsis controlled vocabulary controlled vocabulary specimen material match: pbmcs

specimen_material PBMC preparation GSM7719868 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs PBMCs, Sepsis-3 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Sepsis controlled vocabulary controlled vocabulary specimen material match: pbmcs

specimen_material PBMC preparation GSM7719869 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmcs PBMCs, Sepsis-4 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Sepsis controlled vocabulary controlled vocabulary specimen material match: pbmcs

tissue blood GSE241238 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood dataset_accession: GSE241238 dataset_title: PBMCs from healthy volunteers or septic patients organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true raw_d... controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7719862 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood PBMCs, Healthy-1 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Healthy controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7719863 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood PBMCs, Healthy-2 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Healthy controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7719864 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood PBMCs, Healthy-3 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Healthy controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7719865 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood PBMCs, Healthy-4 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Healthy controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7719866 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood PBMCs, Sepsis-1 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Sepsis controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7719867 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood PBMCs, Sepsis-2 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Sepsis controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7719868 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood PBMCs, Sepsis-3 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Sepsis controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM7719869 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood PBMCs, Sepsis-4 PBMCs cell type: Peripheral Blood Mononuclear Cells; condition: Sepsis controlled vocabulary controlled vocabulary tissue match: blood

Sample Group Preview

8 rows shown Show Hide

Study totals: Case 4 | Control 4 | Unassigned 0 | Excluded 0 | Ambiguous 0 8 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Sepsis or systemic inflammatory response	Case	GSM7719866	PBMCs, Sepsis-1	PBMCs Cell type: Peripheral Blood Mononuclear Cells; Condition: Sepsis	Explicit sample label case marker detected.
Sepsis or systemic inflammatory response	Case	GSM7719867	PBMCs, Sepsis-2	PBMCs Cell type: Peripheral Blood Mononuclear Cells; Condition: Sepsis	Explicit sample label case marker detected.
Sepsis or systemic inflammatory response	Case	GSM7719868	PBMCs, Sepsis-3	PBMCs Cell type: Peripheral Blood Mononuclear Cells; Condition: Sepsis	Explicit sample label case marker detected.
Sepsis or systemic inflammatory response	Case	GSM7719869	PBMCs, Sepsis-4	PBMCs Cell type: Peripheral Blood Mononuclear Cells; Condition: Sepsis	Explicit sample label case marker detected.
Healthy control	Control	GSM7719862	PBMCs, Healthy-1	PBMCs Cell type: Peripheral Blood Mononuclear Cells; Condition: Healthy	Sample-local control marker detected.
Healthy control	Control	GSM7719863	PBMCs, Healthy-2	PBMCs Cell type: Peripheral Blood Mononuclear Cells; Condition: Healthy	Sample-local control marker detected.
Healthy control	Control	GSM7719864	PBMCs, Healthy-3	PBMCs Cell type: Peripheral Blood Mononuclear Cells; Condition: Healthy	Sample-local control marker detected.
Healthy control	Control	GSM7719865	PBMCs, Healthy-4	PBMCs Cell type: Peripheral Blood Mononuclear Cells; Condition: Healthy	Sample-local control marker detected.

Use as Discovery Cohort

External Validation Finder

Carry Siftome's disease, organism, specimen, assay, data type, and accession into a validation project. Uncertain fields remain Unknown.

Summary

Overall design

Source Evidence

Related publications

Metadata Quality Components

Analysis Readiness

Blockers

Next Steps

Analysis Preparation Checklist

Bioinformatician Review

Why This Is Ranked Here

Applied Review Decisions

Derived Classifications

Intent Interpretation

Ranking Facts

Supporting evidence

Cautions

Dataset Warnings

Normalized Fields

Sample Group Preview

Use as Discovery Cohort