GSE186054

Transcriptomic characteristics and impaired immune function of patients with sepsis

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

3 case / 3 control samples elsewhere in the study have incomplete or conflicting evidence; they are not included above

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: 6 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: Wang D, Dai X
Contact name: Dongyao Wang
Submission date: 2021-10-18
Last update: 2022-07-20
Organization: University of Science and Technology of China
Department: Not available
Public date: 2022-07-06
Experiment types: Expression profiling by high throughput sequencing
Platforms: GPL20795 HiSeq X Ten (Homo sapiens)
Series type: Series
SubSeries: Not available
BioProject: PRJNA772247

Summary

Sepsis is a life-threatening condition caused by a dysregulated host response to infection.Although our understanding in the pathophysiological features of sepsis has increased significantly during the past decades, there is still lack of mechanism of sepis.Neutrophils are important regulators against invading pathogens, and their role during sepsis has been studied extensively. However, whether neutrophils could inhibit the immune response of CD8+T cells and the mechanism is unkown in sepsis.

Overall design

Here, 3 sepsis patients and 3 healthy controls were enrolled for analysis of the immunological characteristics of their neutrophils. We sought to comprehensively characterize the transcriptional changes in the two groups by transcriptome sequencing.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 6 GSM samples	Primary source
recount3	Planned trusted source for processed count availability.	Not checked yet
Expression Atlas	Planned source for curated expression experiment links.	Not checked yet
PubMed	Publication context when PubMed identifiers are already known.	Not checked yet

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 3 samples
Likely control group Healthy control 3 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: Infectious disease or host response, Sepsis.
Processed data is available for downstream review.

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

24 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source blood GSM5629814 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5629815 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5629816 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5629817 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5629818 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5629819 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: Blood sample-anatomical-source-v1 sample-local anatomical source

assay_type bulk RNA-seq GSE186054 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence bulk rna-seq dataset_accession: GSE186054 dataset_title: Transcriptomic characteristics and impaired immune function of patients with sepsis organism: Homo sapiens assay_type: bulk RNA-seq p... keyword match keyword match: bulk rna-seq

cell_population neutrophils GSM5629814 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence neutrophils C 1 CD15+CD16+neutrophils tissue: Blood; disease state: sepsis; Sex: Male; age: 33 controlled vocabulary controlled vocabulary cell population match: neutrophils

cell_population neutrophils GSM5629815 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence neutrophils C 5 CD15+CD16+neutrophils tissue: Blood; disease state: sepsis; Sex: Male; age: 28 controlled vocabulary controlled vocabulary cell population match: neutrophils

cell_population neutrophils GSM5629816 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence neutrophils C 3 CD15+CD16+neutrophils tissue: Blood; disease state: sepsis; Sex: Female; age: 36 controlled vocabulary controlled vocabulary cell population match: neutrophils

cell_population neutrophils GSM5629817 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence neutrophils A CD15+CD16+neutrophils tissue: Blood; disease state: Healthy; Sex: Male; age: 28 controlled vocabulary controlled vocabulary cell population match: neutrophils

cell_population neutrophils GSM5629818 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence neutrophils B CD15+CD16+neutrophils tissue: Blood; disease state: Healthy; Sex: Female; age: 25 controlled vocabulary controlled vocabulary cell population match: neutrophils

cell_population neutrophils GSM5629819 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence neutrophils C CD15+CD16+neutrophils tissue: Blood; disease state: Healthy; Sex: Female; age: 31 controlled vocabulary controlled vocabulary cell population match: neutrophils

disease sepsis GSE186054 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence sepsis dataset_accession: GSE186054 dataset_title: Transcriptomic characteristics and impaired immune function of patients with sepsis organism: Homo sapiens assay_type: bulk RNA-seq p... controlled vocabulary controlled vocabulary disease match: sepsis

disease sepsis GSM5629814 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence sepsis C 1 CD15+CD16+neutrophils tissue: Blood; disease state: sepsis; Sex: Male; age: 33 controlled vocabulary controlled vocabulary disease match: sepsis

disease sepsis GSM5629815 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence sepsis C 5 CD15+CD16+neutrophils tissue: Blood; disease state: sepsis; Sex: Male; age: 28 controlled vocabulary controlled vocabulary disease match: sepsis

disease sepsis GSM5629816 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence sepsis C 3 CD15+CD16+neutrophils tissue: Blood; disease state: sepsis; Sex: Female; age: 36 controlled vocabulary controlled vocabulary disease match: sepsis

organism Homo sapiens GSE186054 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE186054 dataset_title: Transcriptomic characteristics and impaired immune function of patients with sepsis organism: Homo sapiens assay_type: bulk RNA-seq p... keyword match keyword match: homo sapiens

tissue blood GSM5629814 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood C 1 CD15+CD16+neutrophils tissue: Blood; disease state: sepsis; Sex: Male; age: 33 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5629815 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood C 5 CD15+CD16+neutrophils tissue: Blood; disease state: sepsis; Sex: Male; age: 28 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5629816 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood C 3 CD15+CD16+neutrophils tissue: Blood; disease state: sepsis; Sex: Female; age: 36 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5629817 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood A CD15+CD16+neutrophils tissue: Blood; disease state: Healthy; Sex: Male; age: 28 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5629818 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood B CD15+CD16+neutrophils tissue: Blood; disease state: Healthy; Sex: Female; age: 25 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5629819 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood C CD15+CD16+neutrophils tissue: Blood; disease state: Healthy; Sex: Female; age: 31 controlled vocabulary controlled vocabulary tissue match: blood

Sample Group Preview

6 rows shown Show Hide

Study totals: Case 3 | Control 3 | Unassigned 0 | Excluded 0 | Ambiguous 0 6 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Sepsis	Case	GSM5629814	C 1	CD15+CD16+neutrophils Tissue: Blood; Disease state: Sepsis; Sex: Male; Age: 33	Case marker detected.
Sepsis	Case	GSM5629815	C 5	CD15+CD16+neutrophils Tissue: Blood; Disease state: Sepsis; Sex: Male; Age: 28	Case marker detected.
Sepsis	Case	GSM5629816	C 3	CD15+CD16+neutrophils Tissue: Blood; Disease state: Sepsis; Sex: Female; Age: 36	Case marker detected.
Healthy control	Control	GSM5629817	A	CD15+CD16+neutrophils Tissue: Blood; Disease state: Healthy; Sex: Male; Age: 28	Sample-local control marker detected.
Healthy control	Control	GSM5629818	B	CD15+CD16+neutrophils Tissue: Blood; Disease state: Healthy; Sex: Female; Age: 25	Sample-local control marker detected.
Healthy control	Control	GSM5629819	C	CD15+CD16+neutrophils Tissue: Blood; Disease state: Healthy; Sex: Female; Age: 31	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.