GSE142607

Metabolism in synovial macrophages are reprogrammed by synovial fibroblasts under inflammatory condition

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

6 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: Mus musculus
Whole-study samples: 9 samples
Specimen: Tissue
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Imai Y, Saeki N
Contact name: Yuuki Imai
Submission date: 2019-12-26
Last update: 2020-12-09
Organization: Ehime University
Department: Proteo-Science Center
Public date: 2020-12-09
Experiment types: Expression profiling by high throughput sequencing
Platforms: GPL16417 Illumina MiSeq (Mus musculus)
Series type: Series
SubSeries: Not available
BioProject: PRJNA597752

Summary

Macrophages have plasticity to adapt microenvironment. In joint tissue, synovial macrophages (SM) and synovial fibroblasts (SF) are maintained in the homeostasis. In Rheumatoid arthritis, crosstalk between SM and SF via inflammatory response induce abnormal activation in respective cells and contribute to disease progression. However, the activation mechanisms in SM which are encouraged by SF are largely unclear. Here, we demonstrated metabolic reprogramming and immunological activation in SM by secretary stimulations from SF using primary culture synovial cell derived from arthritis model mice. To analyze interaction between SM and SF, primary culture of murine synovial cells was performed, respectively. RNA-seq analysis showed SF express abundant secretion-related gene. Thus, we investigated whether conditioned medium from SF (SF-CM) affects biological activity in SM. As the results, SF-CM condition induced both glycolysis and mitochondrial respiration to SM with increased uptake of glucose and glutamine at least, accompanied with cell survival. In addition, several inflammation markers were also upregulated in SM by SF-CM condition. Taken together, these results suggest that metabolic reprogramming were induced in SM by secretory stimulations from SF, followed by activated inflammatory response and long-live. These indicate that such phenotypes of SM may contribute to chronic inflammation in Rheumatoid arthritis

Overall design

mRNA profiles of primary synovial macrophages and synovial fibroblasts obtained from swollen ankle in CAIA mice were generated by deep sequencing, in triplicate, using Illumina Miseq.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 9 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. 1 linked publication 1 DOI Primary publication Reprogramming of synovial macrophage metabolism by synovial fibroblasts under inflammatory conditions. Cell communication and signaling : CCS, 2020 PubMed DOI	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

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 Rheumatoid arthritis Disease context came from Normalization rules.
Likely case group Rheumatoid arthritis 6 samples
Likely control group Healthy control 3 samples

Ranking Facts

Supporting evidence

Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Rheumatoid arthritis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 33256735.
Publication context: Reprogramming of synovial macrophage metabolism by synovial fibroblasts under inflammatory conditions.. Cell communication and signaling : CCS, 2020. PMID 33256735. DOI 10.1186/s12964-020-00678-8.

Cautions

Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
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

31 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source synovium GSM4232802 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence synovial source_name: Primary synovial macrophages sample-anatomical-source-v1 sample-local anatomical source

anatomical_source synovium GSM4232803 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence synovial source_name: Primary synovial macrophages sample-anatomical-source-v1 sample-local anatomical source

anatomical_source synovium GSM4232804 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence synovial source_name: Primary synovial macrophages sample-anatomical-source-v1 sample-local anatomical source

anatomical_source synovium GSM4232805 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence synovial source_name: Primary synovial fibroblasts sample-anatomical-source-v1 sample-local anatomical source

anatomical_source synovium GSM4232806 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence synovial source_name: Primary synovial fibroblasts sample-anatomical-source-v1 sample-local anatomical source

anatomical_source synovium GSM4232807 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence synovial source_name: Primary synovial fibroblasts sample-anatomical-source-v1 sample-local anatomical source

anatomical_source synovium GSM4785646 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence synovial source_name: Primary synovial fibroblasts sample-anatomical-source-v1 sample-local anatomical source

anatomical_source synovium GSM4785647 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence synovial source_name: Primary synovial fibroblasts sample-anatomical-source-v1 sample-local anatomical source

anatomical_source synovium GSM4785648 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence synovial source_name: Primary synovial fibroblasts sample-anatomical-source-v1 sample-local anatomical source

assay_type bulk RNA-seq GSE142607 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence bulk rna-seq dataset_accession: GSE142607 dataset_title: Metabolism in synovial macrophages are reprogrammed by synovial fibroblasts under inflammatory condition organism: Mus musculus assay... keyword match keyword match: bulk rna-seq

disease rheumatoid arthritis GSE142607 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis dataset_accession: GSE142607 dataset_title: Metabolism in synovial macrophages are reprogrammed by synovial fibroblasts under inflammatory condition organism: Mus musculus assay... controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4232802 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis CAIA mice, SM rep1 Primary synovial macrophages strain: C57BL/6; disease state: Collagen Antibody Induced Arthritis (CAIA) model for Rheumatoid Arthritis; cell type: macrophages... controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4232803 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis CAIA mice, SM rep2 Primary synovial macrophages strain: C57BL/6; disease state: Collagen Antibody Induced Arthritis (CAIA) model for Rheumatoid Arthritis; cell type: macrophages... controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4232804 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis CAIA mice, SM rep3 Primary synovial macrophages strain: C57BL/6; disease state: Collagen Antibody Induced Arthritis (CAIA) model for Rheumatoid Arthritis; cell type: macrophages... controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4232805 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis CAIA mice, SF rep1 Primary synovial fibroblasts strain: C57BL/6; disease state: Collagen Antibody Induced Arthritis (CAIA) model for Rheumatoid Arthritis; cell type: fibroblasts... controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4232806 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis CAIA mice, SF rep2 Primary synovial fibroblasts strain: C57BL/6; disease state: Collagen Antibody Induced Arthritis (CAIA) model for Rheumatoid Arthritis; cell type: fibroblasts... controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4232807 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis CAIA mice, SF rep3 Primary synovial fibroblasts strain: C57BL/6; disease state: Collagen Antibody Induced Arthritis (CAIA) model for Rheumatoid Arthritis; cell type: fibroblasts... controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

organism Mus musculus GSE142607 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence mus musculus dataset_accession: GSE142607 dataset_title: Metabolism in synovial macrophages are reprogrammed by synovial fibroblasts under inflammatory condition organism: Mus musculus assay... keyword match keyword match: mus musculus

sample_type normal tissue GSM4785646 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Normal 1 Primary synovial fibroblasts strain: C57BL/6; disease state: normal; cell type: fibroblasts derived from normal ankle tissue; passage: 1 controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM4785647 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Normal 2 Primary synovial fibroblasts strain: C57BL/6; disease state: normal; cell type: fibroblasts derived from normal ankle tissue; passage: 1 controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM4785648 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Normal 3 Primary synovial fibroblasts strain: C57BL/6; disease state: normal; cell type: fibroblasts derived from normal ankle tissue; passage: 1 controlled vocabulary controlled vocabulary sample type match: normal

tissue synovium GSE142607 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence synovial dataset_accession: GSE142607 dataset_title: Metabolism in synovial macrophages are reprogrammed by synovial fibroblasts under inflammatory condition organism: Mus musculus assay... controlled vocabulary controlled vocabulary tissue match: synovial

tissue synovium GSM4232802 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence synovial CAIA mice, SM rep1 Primary synovial macrophages strain: C57BL/6; disease state: Collagen Antibody Induced Arthritis (CAIA) model for Rheumatoid Arthritis; cell type: macrophages... controlled vocabulary controlled vocabulary tissue match: synovial

tissue synovium GSM4232803 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence synovial CAIA mice, SM rep2 Primary synovial macrophages strain: C57BL/6; disease state: Collagen Antibody Induced Arthritis (CAIA) model for Rheumatoid Arthritis; cell type: macrophages... controlled vocabulary controlled vocabulary tissue match: synovial

tissue synovium GSM4232804 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence synovial CAIA mice, SM rep3 Primary synovial macrophages strain: C57BL/6; disease state: Collagen Antibody Induced Arthritis (CAIA) model for Rheumatoid Arthritis; cell type: macrophages... controlled vocabulary controlled vocabulary tissue match: synovial

tissue synovium GSM4232805 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence synovial CAIA mice, SF rep1 Primary synovial fibroblasts strain: C57BL/6; disease state: Collagen Antibody Induced Arthritis (CAIA) model for Rheumatoid Arthritis; cell type: fibroblasts... controlled vocabulary controlled vocabulary tissue match: synovial

tissue synovium GSM4232806 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence synovial CAIA mice, SF rep2 Primary synovial fibroblasts strain: C57BL/6; disease state: Collagen Antibody Induced Arthritis (CAIA) model for Rheumatoid Arthritis; cell type: fibroblasts... controlled vocabulary controlled vocabulary tissue match: synovial

tissue synovium GSM4232807 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence synovial CAIA mice, SF rep3 Primary synovial fibroblasts strain: C57BL/6; disease state: Collagen Antibody Induced Arthritis (CAIA) model for Rheumatoid Arthritis; cell type: fibroblasts... controlled vocabulary controlled vocabulary tissue match: synovial

tissue synovium GSM4785646 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence synovial Normal 1 Primary synovial fibroblasts strain: C57BL/6; disease state: normal; cell type: fibroblasts derived from normal ankle tissue; passage: 1 controlled vocabulary controlled vocabulary tissue match: synovial

tissue synovium GSM4785647 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence synovial Normal 2 Primary synovial fibroblasts strain: C57BL/6; disease state: normal; cell type: fibroblasts derived from normal ankle tissue; passage: 1 controlled vocabulary controlled vocabulary tissue match: synovial

tissue synovium GSM4785648 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence synovial Normal 3 Primary synovial fibroblasts strain: C57BL/6; disease state: normal; cell type: fibroblasts derived from normal ankle tissue; passage: 1 controlled vocabulary controlled vocabulary tissue match: synovial

Sample Group Preview

9 rows shown Show Hide

Study totals: Case 6 | Control 3 | Unassigned 0 | Excluded 0 | Ambiguous 0 9 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Rheumatoid arthritis	Case	GSM4232802	CAIA mice, SM rep1	Primary synovial macrophages Strain: C57BL/6; Disease state: Collagen Antibody Induced Arthritis (CAIA) model for Rheumatoid Arthritis; Cell type: Macrophages derived from CAIA ankle tissue; Passage: 1	Case marker detected.
Rheumatoid arthritis	Case	GSM4232803	CAIA mice, SM rep2	Primary synovial macrophages Strain: C57BL/6; Disease state: Collagen Antibody Induced Arthritis (CAIA) model for Rheumatoid Arthritis; Cell type: Macrophages derived from CAIA ankle tissue; Passage: 1	Case marker detected.
Rheumatoid arthritis	Case	GSM4232804	CAIA mice, SM rep3	Primary synovial macrophages Strain: C57BL/6; Disease state: Collagen Antibody Induced Arthritis (CAIA) model for Rheumatoid Arthritis; Cell type: Macrophages derived from CAIA ankle tissue; Passage: 1	Case marker detected.
Rheumatoid arthritis	Case	GSM4232805	CAIA mice, SF rep1	Primary synovial fibroblasts Strain: C57BL/6; Disease state: Collagen Antibody Induced Arthritis (CAIA) model for Rheumatoid Arthritis; Cell type: Fibroblasts derived from CAIA ankle tissue; Passage: 1	Case marker detected.
Rheumatoid arthritis	Case	GSM4232806	CAIA mice, SF rep2	Primary synovial fibroblasts Strain: C57BL/6; Disease state: Collagen Antibody Induced Arthritis (CAIA) model for Rheumatoid Arthritis; Cell type: Fibroblasts derived from CAIA ankle tissue; Passage: 1	Case marker detected.
Rheumatoid arthritis	Case	GSM4232807	CAIA mice, SF rep3	Primary synovial fibroblasts Strain: C57BL/6; Disease state: Collagen Antibody Induced Arthritis (CAIA) model for Rheumatoid Arthritis; Cell type: Fibroblasts derived from CAIA ankle tissue; Passage: 1	Case marker detected.
Healthy control	Control	GSM4785646	Normal 1	Primary synovial fibroblasts Strain: C57BL/6; Disease state: Normal; Cell type: Fibroblasts derived from normal ankle tissue; Passage: 1	Sample-local control marker detected.
Healthy control	Control	GSM4785647	Normal 2	Primary synovial fibroblasts Strain: C57BL/6; Disease state: Normal; Cell type: Fibroblasts derived from normal ankle tissue; Passage: 1	Sample-local control marker detected.
Healthy control	Control	GSM4785648	Normal 3	Primary synovial fibroblasts Strain: C57BL/6; Disease state: Normal; Cell type: Fibroblasts derived from normal ankle tissue; Passage: 1	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.

Summary

Overall design

Source Evidence

Primary publication

Metadata Quality Components

Analysis Readiness

Blockers

Next Steps

Analysis Preparation Checklist

Bioinformatician Review

Why This Is Ranked Here

Applied Review Decisions

Derived Classifications

Ranking Facts

Supporting evidence

Cautions

Dataset Warnings

Normalized Fields

Sample Group Preview

Use as Discovery Cohort