GSE217700

Analysis of Immune and Prognostic-Related lncRNA PRKCQ-AS1 for Predicting Prognosis and Regulating Effect in 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

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: Ding X, Liang W, Xia H, Liu Y, Liu S, Xia X, Zhu X, Pei Y, Zhang D
Contact name: yongyan pei
Submission date: 2022-11-10
Last update: 2024-04-11
Organization: Guangdong Pharmaceutical University
Department: School of Pharmaceutical and Chemical Engineering
Public date: 2022-11-11
Experiment types: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Series type: Series
SubSeries: Not available
BioProject: PRJNA900185

Summary

Sepsis is a common systemic inflammatory response syndrome caused by infection. It has high mortality and great harm. Long non-coding RNA (lncRNA) has been reported to play a regulatory role in a variety of diseases and is a potential prognostic marker and therapeutic target. However, there are few data on the regulatory effect of lncRNA on sepsis. Therefore, we used transcriptome sequencing and series methods to screen and analyze lncRNAs with potential for prognostic markers in sepsis.we collected 4 sepsis patients whole blood samples and 4 healthy controls whole blood samples for transcriptome sequencing. After quality filtering of the raw sequencing data, we obtained a total of 125.581 Gb Clean Data, the average data amount of each sample was 15.698 Gb, the percentage of Q30 bases was over 93.89%, and the GC content was between 47.53% and 57.54%. Subsequently, we used HISAT2 to align the Clean Data of each sample with the human GRCH38 genome, and the alignment rate was between 96.355% and 97.986%. Through statistics, we found that the obtained lncRNAs were divided into 10 types (figure 1A), among which antisense (36.05%) and lincRNA (33.76%) were the main types.

Overall design

LncRNA and mRNA profiles of 4 sepsis patients whole blood samples and 4 healthy controls whole blood samples

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.	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

Review before analysis

97% 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

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

Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

Next Steps

Review blockers and update sample grouping or dataset selection before analysis.

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

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.

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

Disease context Sepsis, systemic inflammatory response syndrome 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: 20%.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Infectious disease or host response, Sepsis, Systemic inflammatory response syndrome.
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

Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.

Normalized Fields

45 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source blood GSM6725217 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: whle blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM6725218 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: whle blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM6725219 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: whle blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM6725220 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: whle blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM6725221 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: whle blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM6725222 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: whle blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM6725223 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: whle blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM6725224 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence blood tissue: whle blood sample-anatomical-source-v1 sample-local anatomical source

assay_type bulk RNA-seq GSE217700 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence bulk rna-seq dataset_accession: GSE217700 dataset_title: Analysis of Immune and Prognostic-Related lncRNA PRKCQ-AS1 for Predicting Prognosis and Regulating Effect in Sepsis organism: Homo sa... keyword match keyword match: bulk rna-seq

control_type healthy control GSM6725221 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control GP2_1 healthy controls whole blood individual: healthy control 1; tissue: whle blood controlled vocabulary controlled vocabulary control type match: healthy control

control_type healthy control GSM6725222 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control GP2_2 healthy controls whole blood individual: healthy control 2; tissue: whle blood controlled vocabulary controlled vocabulary control type match: healthy control

control_type healthy control GSM6725223 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control GP2_3 healthy controls whole blood individual: healthy control 3; tissue: whle blood controlled vocabulary controlled vocabulary control type match: healthy control

control_type healthy control GSM6725224 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control GP2_4 healthy controls whole blood individual: healthy control 4; tissue: whle blood controlled vocabulary controlled vocabulary control type match: healthy control

disease sepsis GSE217700 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence sepsis dataset_accession: GSE217700 dataset_title: Analysis of Immune and Prognostic-Related lncRNA PRKCQ-AS1 for Predicting Prognosis and Regulating Effect in Sepsis organism: Homo sa... controlled vocabulary controlled vocabulary disease match: sepsis

disease systemic inflammatory response syndrome GSE217700 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence systemic inflammatory response syndrome dataset_accession: GSE217700 dataset_title: Analysis of Immune and Prognostic-Related lncRNA PRKCQ-AS1 for Predicting Prognosis and Regulating Effect in Sepsis organism: Homo sa... controlled vocabulary controlled vocabulary disease match: systemic inflammatory response syndrome

disease sepsis GSM6725217 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence sepsis GP1_1 sepsis patients whole blood individual: sepsis patient 1; tissue: whle blood controlled vocabulary controlled vocabulary disease match: sepsis

disease sepsis GSM6725218 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence sepsis GP1_2 sepsis patients whole blood individual: sepsis patient 2; tissue: whle blood controlled vocabulary controlled vocabulary disease match: sepsis

disease sepsis GSM6725219 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence sepsis GP1_3 sepsis patients whole blood individual: sepsis patient 3; tissue: whle blood controlled vocabulary controlled vocabulary disease match: sepsis

disease sepsis GSM6725220 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence sepsis GP1_4 sepsis patients whole blood individual: sepsis patient 4; tissue: whle blood controlled vocabulary controlled vocabulary disease match: sepsis

normal_tissue_type healthy donor tissue GSM6725221 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control GP2_1 healthy controls whole blood individual: healthy control 1; tissue: whle blood controlled vocabulary controlled vocabulary normal tissue type match: healthy control

normal_tissue_type healthy donor tissue GSM6725222 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control GP2_2 healthy controls whole blood individual: healthy control 2; tissue: whle blood controlled vocabulary controlled vocabulary normal tissue type match: healthy control

normal_tissue_type healthy donor tissue GSM6725223 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control GP2_3 healthy controls whole blood individual: healthy control 3; tissue: whle blood controlled vocabulary controlled vocabulary normal tissue type match: healthy control

normal_tissue_type healthy donor tissue GSM6725224 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control GP2_4 healthy controls whole blood individual: healthy control 4; tissue: whle blood controlled vocabulary controlled vocabulary normal tissue type match: healthy control

organism Homo sapiens GSE217700 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE217700 dataset_title: Analysis of Immune and Prognostic-Related lncRNA PRKCQ-AS1 for Predicting Prognosis and Regulating Effect in Sepsis organism: Homo sa... keyword match keyword match: homo sapiens

sample_type normal tissue GSM6725221 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control GP2_1 healthy controls whole blood individual: healthy control 1; tissue: whle blood controlled vocabulary controlled vocabulary sample type match: healthy control

sample_type normal tissue GSM6725222 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control GP2_2 healthy controls whole blood individual: healthy control 2; tissue: whle blood controlled vocabulary controlled vocabulary sample type match: healthy control

sample_type normal tissue GSM6725223 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control GP2_3 healthy controls whole blood individual: healthy control 3; tissue: whle blood controlled vocabulary controlled vocabulary sample type match: healthy control

sample_type normal tissue GSM6725224 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control GP2_4 healthy controls whole blood individual: healthy control 4; tissue: whle blood controlled vocabulary controlled vocabulary sample type match: healthy control

specimen_material whole blood GSM6725217 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood GP1_1 sepsis patients whole blood individual: sepsis patient 1; tissue: whle blood controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM6725218 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood GP1_2 sepsis patients whole blood individual: sepsis patient 2; tissue: whle blood controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM6725219 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood GP1_3 sepsis patients whole blood individual: sepsis patient 3; tissue: whle blood controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM6725220 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood GP1_4 sepsis patients whole blood individual: sepsis patient 4; tissue: whle blood controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM6725221 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood GP2_1 healthy controls whole blood individual: healthy control 1; tissue: whle blood controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM6725222 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood GP2_2 healthy controls whole blood individual: healthy control 2; tissue: whle blood controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM6725223 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood GP2_3 healthy controls whole blood individual: healthy control 3; tissue: whle blood controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM6725224 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood GP2_4 healthy controls whole blood individual: healthy control 4; tissue: whle blood controlled vocabulary controlled vocabulary specimen material match: whole blood

tissue blood GSE217700 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood dataset_accession: GSE217700 dataset_title: Analysis of Immune and Prognostic-Related lncRNA PRKCQ-AS1 for Predicting Prognosis and Regulating Effect in Sepsis organism: Homo sa... controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM6725217 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood GP1_1 sepsis patients whole blood individual: sepsis patient 1; tissue: whle blood controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM6725218 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood GP1_2 sepsis patients whole blood individual: sepsis patient 2; tissue: whle blood controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM6725219 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood GP1_3 sepsis patients whole blood individual: sepsis patient 3; tissue: whle blood controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM6725220 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood GP1_4 sepsis patients whole blood individual: sepsis patient 4; tissue: whle blood controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM6725221 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood GP2_1 healthy controls whole blood individual: healthy control 1; tissue: whle blood controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM6725222 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood GP2_2 healthy controls whole blood individual: healthy control 2; tissue: whle blood controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM6725223 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood GP2_3 healthy controls whole blood individual: healthy control 3; tissue: whle blood controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM6725224 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood GP2_4 healthy controls whole blood individual: healthy control 4; tissue: whle blood 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	GSM6725217	GP1_1	Sepsis patients whole blood Individual: Sepsis patient 1; Tissue: Whle blood	Explicit sample label case marker detected.
Sepsis or systemic inflammatory response	Case	GSM6725218	GP1_2	Sepsis patients whole blood Individual: Sepsis patient 2; Tissue: Whle blood	Explicit sample label case marker detected.
Sepsis or systemic inflammatory response	Case	GSM6725219	GP1_3	Sepsis patients whole blood Individual: Sepsis patient 3; Tissue: Whle blood	Explicit sample label case marker detected.
Sepsis or systemic inflammatory response	Case	GSM6725220	GP1_4	Sepsis patients whole blood Individual: Sepsis patient 4; Tissue: Whle blood	Explicit sample label case marker detected.
Healthy control	Control	GSM6725221	GP2_1	Healthy controls whole blood Individual: Healthy control 1; Tissue: Whle blood	Sample-local control marker detected.
Healthy control	Control	GSM6725222	GP2_2	Healthy controls whole blood Individual: Healthy control 2; Tissue: Whle blood	Sample-local control marker detected.
Healthy control	Control	GSM6725223	GP2_3	Healthy controls whole blood Individual: Healthy control 3; Tissue: Whle blood	Sample-local control marker detected.
Healthy control	Control	GSM6725224	GP2_4	Healthy controls whole blood Individual: Healthy control 4; Tissue: Whle blood	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.