GSE205672

Transcriptomes of human PBMCs and monocytes in sepsis 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

36 case / 15 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
460 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
Netea M, Riza A, Gat-Viks I, Brandes Leibovitz R
Contact name
Rachel Brandes Leibovitz
Submission date
2022-06-08
Last update
2025-01-29
Organization
Tel Aviv University
Department
Not available
Public date
2025-01-28
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA847153

Summary

FUSE cohort

Overall design

PBMCs and Monocytes from 284 healthy subject and 125 sepsis patients ***Raw data not available due to patient privacy concerns***

Source Evidence

4 sources
Source Contribution Status
GEO

Original dataset metadata, sample metadata, source links, and GEO data availability flags.

Sample records
460 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 161 samples
  • Likely control group Healthy control 299 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: 20%.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Interpreted disease metadata: 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.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

No dataset warnings

Normalized Fields

showing 500 of 2748 fields

Sample Group Preview

showing 100 of 460 preview rows Show Hide
Study totals: Case 161 | Control 299 | Unassigned 0 | Excluded 0 | Ambiguous 0 showing 100 of 460 preview rows
Group Role Accession Title Source / characteristics Reason
Sepsis Case GSM6216895 710055_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216896 710056_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216897 710057_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216898 710058_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216899 710059_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216900 710060_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216901 710061_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216902 710062_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216903 710064_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216904 710065_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216905 710066_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216906 710067_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216907 710068_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216908 710069_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216909 710070_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216910 710071_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216911 710072_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216912 710073_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216913 710074_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216914 710075_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216915 710076_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216916 710077_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216917 710078_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216918 710079_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216919 710080_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216920 710081_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216921 710082_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216922 710083_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216923 710084_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216924 710085_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216925 710086_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216926 710087_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216927 710088_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216928 710089_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216929 710090_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216930 710091_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216931 710092_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216932 710093_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216933 710094_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216934 710095_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216935 710096_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216936 710097_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216937 710098_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216938 710099_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216939 710100_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216940 710101_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216941 710102_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216942 710103_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216943 710104_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
Sepsis Case GSM6216944 710105_PBMC_unstim_SS PBMC Disease state: Sepsis Patient; Cell type: PBMC Case marker detected.
111 additional case samples are hidden from this preview.
Healthy control Control GSM6216611 760086_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216612 760089_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216613 760091_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216614 760093_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216615 760094_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216616 760095_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216617 760096_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216618 760121_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216619 760122_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216620 760193_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216621 760195_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216622 760196_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216623 760197_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216624 760198_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216625 760199_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216626 760200_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216627 760202_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216628 760203_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216629 760205_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216630 760206_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216631 760207_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216632 760208_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216633 760211_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216634 760213_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216635 760214_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216636 760215_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216637 760216_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216638 760217_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216639 760218_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216640 760221_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216641 760222_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216642 760223_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216643 760226_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216644 760227_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216645 760229_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216646 760230_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216647 760231_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216648 760232_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216649 760233_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216650 760235_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216651 760236_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216652 760238_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216653 760240_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216654 760289_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216655 760292_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216656 760298_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216657 760310_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216658 760311_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216659 760312_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
Healthy control Control GSM6216660 760314_PBMC_unstim_HC PBMC Disease state: Healthy control; Cell type: PBMC Sample-local control marker detected.
249 additional control samples are hidden from this preview.

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.