GSE226946

Resident Kupffer cell maladaptation in Liver Fibrosis is Rescued by Monocyte-Derived Syncytia of Macrophages

Whole-study status Not suitable

Dataset does not meet the current suitability threshold.

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 / 5 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: Mus musculus
Whole-study samples: 8 samples
Specimen: Tissue
Reported/interpreted study design: Treatment vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Gordon P
Contact name: Paul Gordon
Submission date: 2023-03-08
Last update: 2024-03-08
Organization: University of Calgary
Department: Not available
Public date: 2024-03-08
Experiment types: Expression profiling by high throughput sequencing
Platforms: GPL19057 Illumina NextSeq 500 (Mus musculus)
Series type: Series
SubSeries: Not available
BioProject: PRJNA942300

Summary

To investigate the effects of liver fobrosis and alteration in liver architecture in the regulation of embryonic Kupffer cells identity and funtion, we used a well stablished carbon tetrachloride model to induce liver fibrosis.

Overall design

Comparative gene expression profiling analysis of data obtained from RNA-seq of naïve KCs and KCs isolated from fibrotic livers.

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	Publication context when PubMed identifiers are already known.	No match found

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: Treatment status metadata normalized where treatment is part of the comparison. 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

90% 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

0/10 pts

Critical warnings must be resolved before downstream analysis.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

Critical dataset warnings must be resolved.

Next Steps

Resolve critical warnings before downstream 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.

Critical dataset warnings are present.

Why This Is Ranked Here

Tumor vs normal

Not suitable Dataset does not meet the current suitability threshold.

Applied Review Decisions

No active review decisions affect this ranking.

Derived Classifications

Organism differs from search intent Mus musculus Search intent expects Homo sapiens. Organism came from Normalization rules.
Disease context Fibrosis, liver fibrosis Disease context came from Normalization rules.
Likely case group Treated 3 samples
Likely control group Untreated 5 samples

Intent Interpretation

Downgrade or exclusion reason Downgraded for tissue search because it is a treatment/control experiment. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

Comparison: Treatment vs control. Specimen: Tissue. Comparison suitability: 0%.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Fibrosis, Liver fibrosis.
Processed data is available for downstream review.

Cautions

Downgraded for tissue search because it is a treatment/control experiment.
Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons.
Overall score capped because comparison suitability is weak for the selected search intent.
Overall score capped because non-human datasets are outside the selected human ranking intent.
Overall score capped because fewer than ten samples limit cohort confidence.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Dataset organism does not match the human patient-tissue tumor-normal intent.

Normalized Fields

32 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source liver GSM7088728 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM7088729 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM7088730 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM7088731 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM7088732 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM7088733 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver fibrosis sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM7088734 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver fibrosis sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM7088735 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver fibrosis sample-anatomical-source-v1 sample-local anatomical source

assay_type bulk RNA-seq GSE226946 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence bulk rna-seq dataset_accession: GSE226946 dataset_title: Resident Kupffer cell maladaptation in Liver Fibrosis is Rescued by Monocyte-Derived Syncytia of Macrophages organism: Mus musculus a... keyword match keyword match: bulk rna-seq

disease fibrosis GSE226946 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis dataset_accession: GSE226946 dataset_title: Resident Kupffer cell maladaptation in Liver Fibrosis is Rescued by Monocyte-Derived Syncytia of Macrophages organism: Mus musculus a... controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSE226946 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver fibrosis dataset_accession: GSE226946 dataset_title: Resident Kupffer cell maladaptation in Liver Fibrosis is Rescued by Monocyte-Derived Syncytia of Macrophages organism: Mus musculus a... controlled vocabulary controlled vocabulary disease match: liver fibrosis

disease fibrosis GSM7088733 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis KCs_treated1 liver fibrosis tissue: liver fibrosis; cell type: liver resident macrophage (Kupffer cells); genotype: Wild-type; treatment: CCl4 controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSM7088733 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver fibrosis KCs_treated1 liver fibrosis tissue: liver fibrosis; cell type: liver resident macrophage (Kupffer cells); genotype: Wild-type; treatment: CCl4 controlled vocabulary controlled vocabulary disease match: liver fibrosis

disease fibrosis GSM7088734 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis KCs_treated2-4 liver fibrosis tissue: liver fibrosis; cell type: liver resident macrophage (Kupffer cells); genotype: Wild-type; treatment: CCl4 controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSM7088734 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver fibrosis KCs_treated2-4 liver fibrosis tissue: liver fibrosis; cell type: liver resident macrophage (Kupffer cells); genotype: Wild-type; treatment: CCl4 controlled vocabulary controlled vocabulary disease match: liver fibrosis

disease fibrosis GSM7088735 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis KCs_treated3 liver fibrosis tissue: liver fibrosis; cell type: liver resident macrophage (Kupffer cells); genotype: Wild-type; treatment: CCl4 controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSM7088735 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver fibrosis KCs_treated3 liver fibrosis tissue: liver fibrosis; cell type: liver resident macrophage (Kupffer cells); genotype: Wild-type; treatment: CCl4 controlled vocabulary controlled vocabulary disease match: liver fibrosis

organism Mus musculus GSE226946 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence mus musculus dataset_accession: GSE226946 dataset_title: Resident Kupffer cell maladaptation in Liver Fibrosis is Rescued by Monocyte-Derived Syncytia of Macrophages organism: Mus musculus a... keyword match keyword match: mus musculus

tissue liver GSE226946 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver dataset_accession: GSE226946 dataset_title: Resident Kupffer cell maladaptation in Liver Fibrosis is Rescued by Monocyte-Derived Syncytia of Macrophages organism: Mus musculus a... controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM7088728 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver KCs_control1 liver tissue: liver; cell type: liver resident macrophage (Kupffer cells); genotype: Wild-type; treatment: control untreated controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM7088729 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver KCs_control2 liver tissue: liver; cell type: liver resident macrophage (Kupffer cells); genotype: Wild-type; treatment: control untreated controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM7088730 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver KCs_control3 liver tissue: liver; cell type: liver resident macrophage (Kupffer cells); genotype: Wild-type; treatment: control untreated controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM7088731 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver KCs_control4 liver tissue: liver; cell type: liver resident macrophage (Kupffer cells); genotype: Wild-type; treatment: control untreated controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM7088732 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver KCs_control5 liver tissue: liver; cell type: liver resident macrophage (Kupffer cells); genotype: Wild-type; treatment: control untreated controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM7088733 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver KCs_treated1 liver fibrosis tissue: liver fibrosis; cell type: liver resident macrophage (Kupffer cells); genotype: Wild-type; treatment: CCl4 controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM7088734 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver KCs_treated2-4 liver fibrosis tissue: liver fibrosis; cell type: liver resident macrophage (Kupffer cells); genotype: Wild-type; treatment: CCl4 controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM7088735 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver KCs_treated3 liver fibrosis tissue: liver fibrosis; cell type: liver resident macrophage (Kupffer cells); genotype: Wild-type; treatment: CCl4 controlled vocabulary controlled vocabulary tissue match: liver

treatment_status untreated GSM7088728 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence untreated KCs_control1 liver tissue: liver; cell type: liver resident macrophage (Kupffer cells); genotype: Wild-type; treatment: control untreated controlled vocabulary controlled vocabulary treatment status match: untreated

treatment_status untreated GSM7088729 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence untreated KCs_control2 liver tissue: liver; cell type: liver resident macrophage (Kupffer cells); genotype: Wild-type; treatment: control untreated controlled vocabulary controlled vocabulary treatment status match: untreated

treatment_status untreated GSM7088730 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence untreated KCs_control3 liver tissue: liver; cell type: liver resident macrophage (Kupffer cells); genotype: Wild-type; treatment: control untreated controlled vocabulary controlled vocabulary treatment status match: untreated

treatment_status untreated GSM7088731 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence untreated KCs_control4 liver tissue: liver; cell type: liver resident macrophage (Kupffer cells); genotype: Wild-type; treatment: control untreated controlled vocabulary controlled vocabulary treatment status match: untreated

treatment_status untreated GSM7088732 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence untreated KCs_control5 liver tissue: liver; cell type: liver resident macrophage (Kupffer cells); genotype: Wild-type; treatment: control untreated controlled vocabulary controlled vocabulary treatment status match: untreated

Sample Group Preview

8 rows shown Show Hide

Study totals: Case 3 | Control 5 | Unassigned 0 | Excluded 0 | Ambiguous 0 8 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Treated	Case	GSM7088733	KCs_treated1	Liver fibrosis Tissue: Liver fibrosis; Cell type: Liver resident macrophage (Kupffer cells); Genotype: Wild-type; Treatment: CCl4	Explicit characteristic comparison arm detected.
Treated	Case	GSM7088734	KCs_treated2-4	Liver fibrosis Tissue: Liver fibrosis; Cell type: Liver resident macrophage (Kupffer cells); Genotype: Wild-type; Treatment: CCl4	Explicit characteristic comparison arm detected.
Treated	Case	GSM7088735	KCs_treated3	Liver fibrosis Tissue: Liver fibrosis; Cell type: Liver resident macrophage (Kupffer cells); Genotype: Wild-type; Treatment: CCl4	Explicit characteristic comparison arm detected.
Untreated	Control	GSM7088728	KCs_control1	Liver Tissue: Liver; Cell type: Liver resident macrophage (Kupffer cells); Genotype: Wild-type; Treatment: Control untreated	Treatment control marker detected.
Untreated	Control	GSM7088729	KCs_control2	Liver Tissue: Liver; Cell type: Liver resident macrophage (Kupffer cells); Genotype: Wild-type; Treatment: Control untreated	Treatment control marker detected.
Untreated	Control	GSM7088730	KCs_control3	Liver Tissue: Liver; Cell type: Liver resident macrophage (Kupffer cells); Genotype: Wild-type; Treatment: Control untreated	Treatment control marker detected.
Untreated	Control	GSM7088731	KCs_control4	Liver Tissue: Liver; Cell type: Liver resident macrophage (Kupffer cells); Genotype: Wild-type; Treatment: Control untreated	Treatment control marker detected.
Untreated	Control	GSM7088732	KCs_control5	Liver Tissue: Liver; Cell type: Liver resident macrophage (Kupffer cells); Genotype: Wild-type; Treatment: Control untreated	Treatment 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.