GSE280813

Licochalcone B alleviates Crohn’s Disease injury by targeting FTO [meRIP-seq]

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 / 6 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: 12 samples
Specimen: Tissue
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Ma D, Liu X, Hong Y, Zhang X
Contact name: duo ma
Submission date: 2024-10-31
Last update: 2024-11-09
Organization: Anhui Medical University
Department: Not available
Public date: 2024-11-09
Experiment types: Other
Platforms: GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Series type: Series
SubSeries: Not available
BioProject: PRJNA1180591

Summary

To investigate the mechanism of demethylase FTO in Crohn's disease，We used m6A MeRIP-seq data from three normal colon samples and three TNBS-induced IBD colon samples of C57 mice for gene expression profiling.

Overall design

Comparative gene expression profiling analysis of m6A MeRIP-seq data from three normal colon samples and three TNBS-induced IBD colon samples of C57 mice

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 12 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: 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 Crohn's disease, inflammatory bowel disease Disease context came from Normalization rules.
Likely case group Inflammatory bowel disease 6 samples
Likely control group Healthy control 6 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: Crohn's disease, Inflammatory bowel disease.
Processed data is available for downstream review.

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.
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

41 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source colon GSM8606109 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM8606110 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM8606111 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM8606112 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM8606113 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM8606114 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM8606115 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM8606116 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM8606117 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM8606118 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM8606119 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM8606120 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

assay_type bulk RNA-seq GSE280813 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence bulk rna-seq dataset_accession: GSE280813 dataset_title: Licochalcone B alleviates Crohn’s Disease injury by targeting FTO [meRIP-seq] organism: Mus musculus assay_type: bulk RNA-seq process... keyword match keyword match: bulk rna-seq

disease Crohn's disease GSE280813 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease dataset_accession: GSE280813 dataset_title: Licochalcone B alleviates Crohn’s Disease injury by targeting FTO [meRIP-seq] organism: Mus musculus assay_type: bulk RNA-seq process... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease inflammatory bowel disease GSE280813 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd dataset_accession: GSE280813 dataset_title: Licochalcone B alleviates Crohn’s Disease injury by targeting FTO [meRIP-seq] organism: Mus musculus assay_type: bulk RNA-seq process... controlled vocabulary controlled vocabulary disease match: ibd

disease inflammatory bowel disease GSM8606112 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd Colonic tissue, M-1, input colon tissue: colon; genotype: WT; treatment: TNBS-induced IBD controlled vocabulary controlled vocabulary disease match: ibd

disease inflammatory bowel disease GSM8606113 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd Colonic tissue, M-2, input colon tissue: colon; genotype: WT; treatment: TNBS-induced IBD controlled vocabulary controlled vocabulary disease match: ibd

disease inflammatory bowel disease GSM8606114 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd Colonic tissue, M-3, input colon tissue: colon; genotype: WT; treatment: TNBS-induced IBD controlled vocabulary controlled vocabulary disease match: ibd

disease inflammatory bowel disease GSM8606118 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd Colonic tissue, M-1, IP colon tissue: colon; genotype: WT; treatment: TNBS-induced IBD controlled vocabulary controlled vocabulary disease match: ibd

disease inflammatory bowel disease GSM8606119 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd Colonic tissue, M-2, IP colon tissue: colon; genotype: WT; treatment: TNBS-induced IBD controlled vocabulary controlled vocabulary disease match: ibd

disease inflammatory bowel disease GSM8606120 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd Colonic tissue, M-3, IP colon tissue: colon; genotype: WT; treatment: TNBS-induced IBD controlled vocabulary controlled vocabulary disease match: ibd

organism Mus musculus GSE280813 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence mus musculus dataset_accession: GSE280813 dataset_title: Licochalcone B alleviates Crohn’s Disease injury by targeting FTO [meRIP-seq] organism: Mus musculus assay_type: bulk RNA-seq process... keyword match keyword match: mus musculus

sample_type normal tissue GSM8606109 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Colonic tissue, N-1, input colon tissue: colon; genotype: WT; treatment: Normal feeding controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM8606110 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Colonic tissue, N-2, input colon tissue: colon; genotype: WT; treatment: Normal feeding controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM8606111 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Colonic tissue, N-3, input colon tissue: colon; genotype: WT; treatment: Normal feeding controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM8606115 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Colonic tissue, N-1, IP colon tissue: colon; genotype: WT; treatment: Normal feeding controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM8606116 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Colonic tissue, N-2, IP colon tissue: colon; genotype: WT; treatment: Normal feeding controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM8606117 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Colonic tissue, N-3, IP colon tissue: colon; genotype: WT; treatment: Normal feeding controlled vocabulary controlled vocabulary sample type match: normal

tissue colon GSE280813 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon dataset_accession: GSE280813 dataset_title: Licochalcone B alleviates Crohn’s Disease injury by targeting FTO [meRIP-seq] organism: Mus musculus assay_type: bulk RNA-seq process... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM8606109 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colonic tissue, N-1, input colon tissue: colon; genotype: WT; treatment: Normal feeding controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM8606110 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colonic tissue, N-2, input colon tissue: colon; genotype: WT; treatment: Normal feeding controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM8606111 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colonic tissue, N-3, input colon tissue: colon; genotype: WT; treatment: Normal feeding controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM8606112 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colonic tissue, M-1, input colon tissue: colon; genotype: WT; treatment: TNBS-induced IBD controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM8606113 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colonic tissue, M-2, input colon tissue: colon; genotype: WT; treatment: TNBS-induced IBD controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM8606114 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colonic tissue, M-3, input colon tissue: colon; genotype: WT; treatment: TNBS-induced IBD controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM8606115 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colonic tissue, N-1, IP colon tissue: colon; genotype: WT; treatment: Normal feeding controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM8606116 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colonic tissue, N-2, IP colon tissue: colon; genotype: WT; treatment: Normal feeding controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM8606117 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colonic tissue, N-3, IP colon tissue: colon; genotype: WT; treatment: Normal feeding controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM8606118 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colonic tissue, M-1, IP colon tissue: colon; genotype: WT; treatment: TNBS-induced IBD controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM8606119 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colonic tissue, M-2, IP colon tissue: colon; genotype: WT; treatment: TNBS-induced IBD controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM8606120 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colonic tissue, M-3, IP colon tissue: colon; genotype: WT; treatment: TNBS-induced IBD controlled vocabulary controlled vocabulary tissue match: colon

Sample Group Preview

12 rows shown Show Hide

Study totals: Case 6 | Control 6 | Unassigned 0 | Excluded 0 | Ambiguous 0 12 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Inflammatory bowel disease	Case	GSM8606112	Colonic tissue, M-1, input	Colon Tissue: Colon; Genotype: WT; Treatment: TNBS-induced IBD	Disease-state value stored under a treatment-labelled characteristic detected.
Inflammatory bowel disease	Case	GSM8606113	Colonic tissue, M-2, input	Colon Tissue: Colon; Genotype: WT; Treatment: TNBS-induced IBD	Disease-state value stored under a treatment-labelled characteristic detected.
Inflammatory bowel disease	Case	GSM8606114	Colonic tissue, M-3, input	Colon Tissue: Colon; Genotype: WT; Treatment: TNBS-induced IBD	Disease-state value stored under a treatment-labelled characteristic detected.
Inflammatory bowel disease	Case	GSM8606118	Colonic tissue, M-1, IP	Colon Tissue: Colon; Genotype: WT; Treatment: TNBS-induced IBD	Disease-state value stored under a treatment-labelled characteristic detected.
Inflammatory bowel disease	Case	GSM8606119	Colonic tissue, M-2, IP	Colon Tissue: Colon; Genotype: WT; Treatment: TNBS-induced IBD	Disease-state value stored under a treatment-labelled characteristic detected.
Inflammatory bowel disease	Case	GSM8606120	Colonic tissue, M-3, IP	Colon Tissue: Colon; Genotype: WT; Treatment: TNBS-induced IBD	Disease-state value stored under a treatment-labelled characteristic detected.
Healthy control	Control	GSM8606109	Colonic tissue, N-1, input	Colon Tissue: Colon; Genotype: WT; Treatment: Normal feeding	Explicit characteristic control arm detected.
Healthy control	Control	GSM8606110	Colonic tissue, N-2, input	Colon Tissue: Colon; Genotype: WT; Treatment: Normal feeding	Explicit characteristic control arm detected.
Healthy control	Control	GSM8606111	Colonic tissue, N-3, input	Colon Tissue: Colon; Genotype: WT; Treatment: Normal feeding	Explicit characteristic control arm detected.
Healthy control	Control	GSM8606115	Colonic tissue, N-1, IP	Colon Tissue: Colon; Genotype: WT; Treatment: Normal feeding	Explicit characteristic control arm detected.
Healthy control	Control	GSM8606116	Colonic tissue, N-2, IP	Colon Tissue: Colon; Genotype: WT; Treatment: Normal feeding	Explicit characteristic control arm detected.
Healthy control	Control	GSM8606117	Colonic tissue, N-3, IP	Colon Tissue: Colon; Genotype: WT; Treatment: Normal feeding	Explicit characteristic control arm 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.