GSE137340

Blood transcriptome of human sepsis in an Indian cohort [Illumina array]

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
microarray
Organism
Homo sapiens
Whole-study samples
57 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
Mukhopadhay S, Mohapatra SK, Mukhopadhyay S
Contact name
SAMANWOY MUKHOPADHYAY
Submission date
2019-09-12
Last update
2022-09-13
Organization
NATIONAL INSTITUTE OF BIOMEDICAL GENOMICS
Department
skm_lab
Public date
2022-09-12
Experiment types
Expression profiling by array
Platforms
GPL10558 Illumina HumanHT-12 V4.0 expression beadchip
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA565215

Summary

Sepsis remains a lethal ailment with imprecise treatment and ill-understood biology. A clinical transcriptomic analysis of sepsis patients was performed for the first time in India and revealed large-scale change in blood gene expression in patients of severe sepsis and septic shock admitted to ICU. Three biological processes were quantified using scores derived from the corresponding transcriptional modules. Comparison of the module scores revealed that genes associated with immune response were more suppressed compared to the inflammation-associated genes. These findings will have great implication in the treatment and prognosis of severe sepsis/septic shock if translated into a bedside tool.

Overall design

Transcriptomic profiling was performed on sepsis cases and on matched (by age and gender) healthy controls, who were not suffering from any inflammatory diseases, and were not related to the patients. Samples were collected at two different time points in the cases. Two blood samples from the sepsis cases were collected, the first at the time of diagnosis (D1), and a second sample after 24 hours (D2) . Representative single blood sample was collected from each of the healthy control individuals. A total of 27 patients (23 with paired transcriptome data for two time points) and 12 healthy control subjects (for the single time point) were recruited in this study.

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
57 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.

4 linked publications 4 DOIs

Related publications

  1. LCN2 and ELANE overexpression induces sepsis. Medicine, 2024
  2. Integrated bioinformatics analysis of molecular signatures and therapeutic targets in early sepsis. Frontiers in cellular and infection microbiology, 2026
  3. Comprehensive integration of diagnostic biomarker analysis and immune cell infiltration features in sepsis via machine learning and bioinformatics techniques. Frontiers in immunology, 2025
  4. [Exploration of key ferroptosis-related genes as therapeutic targets for sepsis based on bioinformatics and the depiction of their immune profiles characterization]. Zhonghua wei zhong bing ji jiu yi xue, 2024
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

Review before analysis
85% 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

3/15 pts

Unassigned or review-needed samples remain before analysis.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

  • 2 samples are still unassigned.
  • 2 samples need manual grouping review.

Next Steps

  • Resolve unassigned or review-needed samples in the grouping table.

Analysis Preparation Checklist

4/6 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

Needs review

2 review-needed samples and 2 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

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

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

Analysis readiness has blockers that must be resolved before DE.

One or more samples are unassigned and need manual grouping decisions.

One or more samples were flagged for manual review.

Assay context may require expert handling before DESeq2-style analysis.

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

  • Assay differs from search intent Microarray Search intent expects bulk RNA-seq. Assay came from Normalization rules.
  • Disease context Sepsis, septic shock, severe sepsis Disease context came from Normalization rules.
  • Likely case group Sepsis or systemic inflammatory response 43 samples
  • Likely control group Healthy control 12 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%.
  • Interpreted disease metadata: Sepsis, Septic shock, Severe sepsis.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 4 publications; 4 DOIs available: PMID 38363924, PMID 39586719, PMID 40129981, PMID 41947789.
  • Publication context: LCN2 and ELANE overexpression induces sepsis.. Medicine, 2024. PMID 38363924. DOI 10.1097/MD.0000000000037255.
  • Publication context: [Exploration of key ferroptosis-related genes as therapeutic targets for sepsis based on bioinformatics and the depiction of their immune profiles characterization].. Zhonghua wei zhong bing ji jiu yi xue, 2024. PMID 39586719. DOI 10.3760/cma.j.cn121430-20240524-00457.
  • Publication context: Comprehensive integration of diagnostic biomarker analysis and immune cell infiltration features in sepsis via machine learning and bioinformatics techniques.. Frontiers in immunology, 2025. PMID 40129981. DOI 10.3389/fimmu.2025.1526174.
  • Publication context: 1 additional linked PubMed publications are available.

Cautions

  • Downgraded for tissue search because it is a biofluid cohort.
  • Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
  • 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

Normalized Fields

246 fields

Sample Group Preview

57 rows shown Show Hide
Study totals: Case 43 | Control 12 | Unassigned 0 | Excluded 0 | Ambiguous 2 57 rows shown
Group Role Accession Title Source / characteristics Reason
Sepsis or systemic inflammatory response Case GSM4075768 1D1 Subject 1, Severe Sepsis,Day 1 Tissue: Whole blood; Age: 20; Sex: M; Diagnosis: Severe Sepsis; Time of sample collection: 0 hr; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075769 1D2 Subject 1, Severe Sepsis,Day 2 Tissue: Whole blood; Age: 20; Sex: M; Diagnosis: Severe Sepsis; Time of sample collection: 24 hrs; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075770 5D1 Subject 5, Septic Shock, Day 1 Tissue: Whole blood; Age: 70; Sex: M; Diagnosis: Septic Shock; Time of sample collection: 0 hr; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075771 5D2 Subject 5, Septic Shock, Day 2 Tissue: Whole blood; Age: 70; Sex: M; Diagnosis: Septic Shock; Time of sample collection: 24 hrs; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075772 6D1 Subject 6, Septic Shock, Day 1 Tissue: Whole blood; Age: 55; Sex: F; Diagnosis: Septic Shock; Time of sample collection: 0 hr; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075773 6D2 Subject 6, Septic Shock, Day 2 Tissue: Whole blood; Age: 55; Sex: F; Diagnosis: Septic Shock; Time of sample collection: 24 hrs; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075774 8D1 Subject 8, Severe Sepsis, Day 1 Tissue: Whole blood; Age: 29; Sex: M; Diagnosis: Severe Sepsis; Time of sample collection: 0 hr; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075775 8D2 Subject 8, Severe Sepsis, Day 2 Tissue: Whole blood; Age: 29; Sex: M; Diagnosis: Severe Sepsis; Time of sample collection: 24 hrs; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075776 10D1 Subject 10, Severe Sepsis, Day 1 Tissue: Whole blood; Age: 65; Sex: M; Diagnosis: Severe Sepsis; Time of sample collection: 0 hr; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075777 19D1 Subject 19, Septic Shock,Day 1 Tissue: Whole blood; Age: 14; Sex: F; Diagnosis: Septic Shock; Time of sample collection: 0 hr; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075778 19D2 Subject 19, Septic Shock,Day 2 Tissue: Whole blood; Age: 14; Sex: F; Diagnosis: Septic Shock; Time of sample collection: 24 hrs; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075779 21D2 Subject 21, Septic Shock, Day 2 Tissue: Whole blood; Age: 20; Sex: M; Diagnosis: Septic Shock; Time of sample collection: 24 hrs; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075780 31D1 Subject 31, Severe Sepsis, Day 1 Tissue: Whole blood; Age: 73; Sex: M; Diagnosis: Severe Sepsis; Time of sample collection: 0 hr; Outcome: Died Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075781 31D2 Subject 31, Severe Sepsis, Day 2 Tissue: Whole blood; Age: 73; Sex: M; Diagnosis: Severe Sepsis; Time of sample collection: 24 hrs; Outcome: Died Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075782 32D1 Subject 32, Severe Sepsis, Day 1 Tissue: Whole blood; Age: 30; Sex: F; Diagnosis: Severe Sepsis; Time of sample collection: 0 hr; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075783 32D2 Subject 32, Severe Sepsis, Day 2 Tissue: Whole blood; Age: 30; Sex: F; Diagnosis: Severe Sepsis; Time of sample collection: 24 hrs; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075784 34D1 Subject 34, Septic Shock, Day 1 Tissue: Whole blood; Age: 32; Sex: M; Diagnosis: Septic Shock; Time of sample collection: 0 hr; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075785 34D2 Subject 34, Septic Shock, Day 2 Tissue: Whole blood; Age: 32; Sex: M; Diagnosis: Septic Shock; Time of sample collection: 24 hrs; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075786 42D1 Subject 42, Severe Sepsis, Day 1 Tissue: Whole blood; Age: 18; Sex: M; Diagnosis: Severe Sepsis; Time of sample collection: 0 hr; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075787 42D2 Subject 42, Severe Sepsis, Day 2 Tissue: Whole blood; Age: 18; Sex: M; Diagnosis: Severe Sepsis; Time of sample collection: 24 hrs; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075788 57D1 Subject 57, Sepsis, Day 1 Tissue: Whole blood; Age: 30; Sex: M; Diagnosis: Sepsis; Time of sample collection: 0 hr; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075789 57D2 Subject 57, Sepsis, Day 2 Tissue: Whole blood; Age: 30; Sex: M; Diagnosis: Sepsis; Time of sample collection: 24 hrs; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075790 58D1 Subject 58, Sepsis, Day 1 Tissue: Whole blood; Age: 85; Sex: M; Diagnosis: Sepsis; Time of sample collection: 0 hr; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075791 58D2 Subject 58, Sepsis, Day 2 Tissue: Whole blood; Age: 85; Sex: M; Diagnosis: Sepsis; Time of sample collection: 24 hrs; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075792 60D1 Subject 60, Severe Sepsis, Day 1 Tissue: Whole blood; Age: 39; Sex: M; Diagnosis: Severe Sepsis; Time of sample collection: 0 hr; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075793 60D2 Subject 60, Severe Sepsis, Day 2 Tissue: Whole blood; Age: 39; Sex: M; Diagnosis: Severe Sepsis; Time of sample collection: 24 hrs; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075794 61D1 Subject 61, Severe Sepsis, Day 1 Tissue: Whole blood; Age: 50; Sex: F; Diagnosis: Severe Sepsis; Time of sample collection: 0 hr; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075795 61D2 Subject 61, Severe Sepsis, Day 2 Tissue: Whole blood; Age: 50; Sex: F; Diagnosis: Severe Sepsis; Time of sample collection: 24 hrs; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075796 62D1 Subject 62, Severe Sepsis,Day 1 Tissue: Whole blood; Age: 45; Sex: M; Diagnosis: Severe Sepsis; Time of sample collection: 0 hr; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075797 62D2 Subject 62, Severe Sepsis,Day 2 Tissue: Whole blood; Age: 45; Sex: M; Diagnosis: Severe Sepsis; Time of sample collection: 24 hrs; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075798 63D1 Subject 63, Severe Sepsis, Day 1 Tissue: Whole blood; Age: 33; Sex: M; Diagnosis: Severe Sepsis; Time of sample collection: 0 hr; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075799 63D2 Subject 63, Severe Sepsis, Day 2 Tissue: Whole blood; Age: 33; Sex: M; Diagnosis: Severe Sepsis; Time of sample collection: 24 hrs; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075800 54D2 Subject 54, Septic Shock, Day 2 Tissue: Whole blood; Age: 38; Sex: F; Diagnosis: Septic Shock; Time of sample collection: 24 hrs; Outcome: Died Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075801 56D1 Subject 56, Septic Shock, Day 1 Tissue: Whole blood; Age: 63; Sex: F; Diagnosis: Septic Shock; Time of sample collection: 0 hr; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075802 59D2 Subject 59, Severe Sepsis, Day 2 Tissue: Whole blood; Age: 70; Sex: M; Diagnosis: Severe Sepsis; Time of sample collection: 24 hrs; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075805 55D1 Subject 55, Severe Sepsis,Day 1 Tissue: Whole blood; Age: 63; Sex: F; Diagnosis: Severe Sepsis; Time of sample collection: 0 hr; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075806 55D2 Subject 55, Severe Sepsis,Day 2 Tissue: Whole blood; Age: 63; Sex: F; Diagnosis: Severe Sepsis; Time of sample collection: 24 hrs; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075807 14D1 Subject 14, Severe Sepsis, Day 1 Tissue: Whole blood; Age: 38; Sex: F; Diagnosis: Severe Sepsis; Time of sample collection: 0 hr; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075808 14D2 Subject 14, Severe Sepsis, Day 2 Tissue: Whole blood; Age: 38; Sex: F; Diagnosis: Severe Sepsis; Time of sample collection: 24 hrs; Outcome: Survived Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075809 90D1 Subject 90, Severe Sepsis, Day 1 Tissue: Whole blood; Age: 42; Sex: M; Diagnosis: Severe Sepsis; Time of sample collection: 0 hr; Outcome: NA Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075810 90D2 Subject 90, Severe Sepsis, Day 2 Tissue: Whole blood; Age: 42; Sex: M; Diagnosis: Severe Sepsis; Time of sample collection: 24 hrs; Outcome: NA Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075811 70D1 Subject 70, Septic Shock, Day 1 Tissue: Whole blood; Age: 50; Sex: M; Diagnosis: Septic Shock; Time of sample collection: 0 hr; Outcome: NA Explicit sample label case marker detected.
Sepsis or systemic inflammatory response Case GSM4075812 70D2 Subject 70, Septic Shock, Day 2 Tissue: Whole blood; Age: 50; Sex: M; Diagnosis: Septic Shock; Time of sample collection: 24 hrs; Outcome: NA Explicit sample label case marker detected.
Healthy control Control GSM4075813 Ctrl_sm Subject C1, Healthy Tissue: Whole blood; Age: 26; Sex: M; Diagnosis: Healthy; Time of sample collection: NA; Outcome: Survived Sample-local control marker detected.
Healthy control Control GSM4075814 C4 Subject C4, Healthy Tissue: Whole blood; Age: 40; Sex: F; Diagnosis: Healthy; Time of sample collection: 0 hr; Outcome: Survived Sample-local control marker detected.
Healthy control Control GSM4075815 C7 Subject C7, Healthy Tissue: Whole blood; Age: 40; Sex: M; Diagnosis: Healthy; Time of sample collection: 0 hr; Outcome: Survived Sample-local control marker detected.
Healthy control Control GSM4075816 C8 Subject C8, Healthy Tissue: Whole blood; Age: 22; Sex: M; Diagnosis: Healthy; Time of sample collection: 0 hr; Outcome: Survived Sample-local control marker detected.
Healthy control Control GSM4075817 C9 Subject C9, Healthy Tissue: Whole blood; Age: 40; Sex: F; Diagnosis: Healthy; Time of sample collection: 0 hr; Outcome: Survived Sample-local control marker detected.
Healthy control Control GSM4075818 C10 Subject C10, Healthy Tissue: Whole blood; Age: 44; Sex: M; Diagnosis: Healthy; Time of sample collection: 0 hr; Outcome: Survived Sample-local control marker detected.
Healthy control Control GSM4075819 C11 Subject C11, Healthy Tissue: Whole blood; Age: 20; Sex: M; Diagnosis: Healthy; Time of sample collection: 0 hr; Outcome: Survived Sample-local control marker detected.
Healthy control Control GSM4075820 C12 Subject C12, Healthy Tissue: Whole blood; Age: 50; Sex: F; Diagnosis: Healthy; Time of sample collection: 0 hr; Outcome: Survived Sample-local control marker detected.
Healthy control Control GSM4075821 C17 Subject C17, Healthy Tissue: Whole blood; Age: 40; Sex: M; Diagnosis: Healthy; Time of sample collection: 0 hr; Outcome: Survived Sample-local control marker detected.
Healthy control Control GSM4075822 C18 Subject C18, Healthy Tissue: Whole blood; Age: 50; Sex: M; Diagnosis: Healthy; Time of sample collection: 0 hr; Outcome: Survived Sample-local control marker detected.
Healthy control Control GSM4075823 C20 Subject C20, Healthy Tissue: Whole blood; Age: 22; Sex: F; Diagnosis: Healthy; Time of sample collection: 0 hr; Outcome: Survived Sample-local control marker detected.
Healthy control Control GSM4075824 C21 Suject C21, Healthy Tissue: Whole blood; Age: 45; Sex: M; Diagnosis: Healthy; Time of sample collection: 0 hr; Outcome: Survived Sample-local control marker detected.
Unassigned Ambiguous GSM4075803 65D1 Subject 65, Day 1 Tissue: Whole blood; Age: NA; Sex: NA; Diagnosis: NA; Time of sample collection: 0 hr; Outcome: Survived ambiguous sample: Ambiguous case/control metadata detected.
Unassigned Ambiguous GSM4075804 66D1 Subject 66, Day 1 Tissue: Whole blood; Age: NA; Sex: NA; Diagnosis: NA; Time of sample collection: 0 hr; Outcome: Survived ambiguous sample: Ambiguous case/control metadata 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.