GSE150883

Influence of Liver Fibrosis on Pien Tze Huang by RNA-Seq Analysis of Circular RNAs

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
Treatment vs control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Qin S, Wang T, Zhu J
Contact name
Jinhang Zhu
Submission date
2020-05-19
Last update
2022-09-27
Organization
Shanghai Jiao Tong University
Department
Not available
Public date
2021-03-01
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Series type
Series
SubSeries
Not available
BioProject
PRJNA633910

Summary

Purpose: We investigate the regulation circRNAs in the damaged fibrotic liver treated with Pien Tze Huang (PZH) by RNA-seq. Methods: Liver tissue circRNAs expression profiles from 8-week carbon tetrachloride (CCl4)-induced, and PZH-treated and CCl4-induced liver fibrosis control mice were investigated by RNA-seq and dysregulated circRNAs in PZH-treated were identified. Various bioinformatics analyses established competing endogenous RNA (ceNRA) in circRNAs-miRNAs-mRNAs axis. Moreover, GO annotation and Kegg pathway were analyzed to identify the relational biological processes and pathway. qRT–PCR validation was performed using LX-2 cell sample pairs and SYBR Green assays. Results: We identified 91 differentially expressed circRNAs in the PZH-treated compared with control mice, of which 58 up-regulated circRNAs and 43 down-regulated circRNAs. The ceRNA network were constructed suggesting the potential role of circRNAs is the regulation of target gene expression as a miRNAs sponge. Moreover, GO and Kegg pathway analysis showed that these predicted mRNAs were related to liver fibrosis-related pathways such as TNF, PI3K-Akt, and MAPK signaling pathway. Meanwhile, the results of validation qRT-PCR of target genes in LX-2 cells were in accordance with RNA-seq with high confidence. Conclusions: We identified the dysregulated circRNAs and established functional network of circRNA-miRNA-mRNA to further reveal the potential interactions and biological processes in PZH-treated liver fibrosis mice. These findings indicate that mmu_circ_Slc25a25 may modulate the transcription of certain genes, such as Slc7a11 and Slc39a14, which may provide a more precise and comprehensive perspective for clarifying the role of PZH therapy as a potential agent for treatment of liver fibrosis.

Overall design

Investigation of dysregulated circRNA in liver tissue of 8-week PZH-treated or without mice by RNA-seq, using Illumina Hiseq 4000.

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

Primary GEO citations and related PubMed articles that mention this dataset.

1 linked publication 1 DOI

Primary publication

  1. Identification of circular RNA biomarkers for Pien Tze Huang treatment of CCl4‑induced liver fibrosis using RNA‑sequencing. Molecular medicine reports, 2022
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.
  • Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

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.

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

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 6 samples
  • Likely control group Control 6 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.
  • External evidence: PubMed links 1 publication; 1 DOI available: PMID 36004475.
  • Publication context: Identification of circular RNA biomarkers for Pien Tze Huang treatment of CCl4‑induced liver fibrosis using RNA‑sequencing.. Molecular medicine reports, 2022. PMID 36004475. DOI 10.3892/mmr.2022.12825.

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.
  • Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
  • 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 secondary RNA assays are not primary mRNA tissue RNA-seq.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Normalized Fields

53 fields

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
Treated Case GSM4560123 PZH 1 Liver Strain: C57BL/8; Tissue: Liver; Disease: Carbon tetrachloride (CCl4)-induced liver fibrosis; Treatment: Pien Tze Huang (PZH) Explicit characteristic comparison arm detected.
Treated Case GSM4560124 PZH 2 Liver Strain: C57BL/8; Tissue: Liver; Disease: Carbon tetrachloride (CCl4)-induced liver fibrosis; Treatment: Pien Tze Huang (PZH) Explicit characteristic comparison arm detected.
Treated Case GSM4560125 PZH 3 Liver Strain: C57BL/8; Tissue: Liver; Disease: Carbon tetrachloride (CCl4)-induced liver fibrosis; Treatment: Pien Tze Huang (PZH) Explicit characteristic comparison arm detected.
Treated Case GSM4560126 PZH 4 Liver Strain: C57BL/8; Tissue: Liver; Disease: Carbon tetrachloride (CCl4)-induced liver fibrosis; Treatment: Pien Tze Huang (PZH) Explicit characteristic comparison arm detected.
Treated Case GSM4560127 PZH 5 Liver Strain: C57BL/8; Tissue: Liver; Disease: Carbon tetrachloride (CCl4)-induced liver fibrosis; Treatment: Pien Tze Huang (PZH) Explicit characteristic comparison arm detected.
Treated Case GSM4560128 PZH 6 Liver Strain: C57BL/8; Tissue: Liver; Disease: Carbon tetrachloride (CCl4)-induced liver fibrosis; Treatment: Pien Tze Huang (PZH) Explicit characteristic comparison arm detected.
Control Control GSM4560129 Control 1 Liver Strain: C57BL/8; Tissue: Liver; Disease: Carbon tetrachloride (CCl4)-induced liver fibrosis; Treatment: Control Explicit characteristic control arm detected.
Control Control GSM4560130 Control 2 Liver Strain: C57BL/8; Tissue: Liver; Disease: Carbon tetrachloride (CCl4)-induced liver fibrosis; Treatment: Control Explicit characteristic control arm detected.
Control Control GSM4560131 Control 3 Liver Strain: C57BL/8; Tissue: Liver; Disease: Carbon tetrachloride (CCl4)-induced liver fibrosis; Treatment: Control Explicit characteristic control arm detected.
Control Control GSM4560132 Control 4 Liver Strain: C57BL/8; Tissue: Liver; Disease: Carbon tetrachloride (CCl4)-induced liver fibrosis; Treatment: Control Explicit characteristic control arm detected.
Control Control GSM4560133 Control 5 Liver Strain: C57BL/8; Tissue: Liver; Disease: Carbon tetrachloride (CCl4)-induced liver fibrosis; Treatment: Control Explicit characteristic control arm detected.
Control Control GSM4560134 Control 6 Liver Strain: C57BL/8; Tissue: Liver; Disease: Carbon tetrachloride (CCl4)-induced liver fibrosis; Treatment: Control 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.