GSE23996

Treg_Chip_Expression_Profile_Healthy_vs_Crohns_Disease

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 / 29 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
microarray
Organism
Homo sapiens
Whole-study samples
35 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
Geffers R, Pfoertner S, Maul J
Contact name
Robert Geffers
Submission date
2010-09-07
Last update
2012-12-31
Organization
HCI - Helmholtz Centre for Infection Research
Department
Dep. Molecular Bacteriology
Public date
2012-12-31
Experiment types
Expression profiling by array
Platforms
GPL10887 HCI Human TReg Chip
Series type
Series
SubSeries
Not available
BioProject
PRJNA130289

Summary

Regulatory T cells from patients with Crohn´s disease show an inadequate increase of their frequency in inflamed mucosa. Using a self-developed mRNA-array (Treg Chip), we wanted to identified candidate genes for a disturbed Treg migration Keywords: cell type comparison

Overall design

To obtain individual transcription profiles, we isolated CD4+CD25+ and CD4+CD25- T cells from peripheral blood of 6 patients with Crohn´s disease (3 patients each with active (aCD) and inactive disease (iCD)) and 11 healthy control (HC) using magnetic cell sorting. Micoarray analysis was done using our self-developped human TReg Chip. RNA from CD4+CD25+ T cells was isolated. After ethanol precipitation, quality and integrity of the total RNA was controlled. Samples were prepared by applying a double-linear amplification method. Briefly, the first round of RNA-amplification was performed without biotinylated nucleotides. After clean-up of the precipitated aRNA synthesis of second round, first-strand cDNA. Subsequent second-strand cDNA was prepared like in the first round but integrating an additional RNAse H incubation step to digest the aRNA before annealing of the T7T23V primer. The second round of RNA amplification was performed as an in vitro transcription assay in the presence of biotinylated UTP. The concentration of the obtained biotin-labelled cRNA was determined by UV absorbance and its quality as means of product length distribution was again checked. In all cases, 15 µg of each biotinylated cRNA preparation were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre). Samples were hybridized to individual Human TReg Chips for 16 hours at 42°C. After hybridisation the microarrays were washed, stained with Cy5-streptavidin and read . Signal intensities were qualified and quantified by means. Spots of poor quality (flag = 3) were excluded from further analysis. To adjust arrays from different experiments, data normalisation based on median signal intensities of the housekeeping genes was carried out. In addition, to adjust the data set from HC (11 donors, 29 chips) to aCD or iCD (3 patients each, 6 chips), median normalised signal intensity for each gene and donor was calculated (MV), standard derivation (SD) was assigned and normalised (CV = SD/MV). Statistical Analysis of Microarrays (SAM) was used to ascertain gene expression changes in CD4+CD25+ regulatory and CD4+CD25- naïve T cells. For this, only genes with a CV < 0.3 in 8/11 HC were evaluated.

Source Evidence

4 sources
Source Contribution Status
GEO

Original dataset metadata, sample metadata, source links, and GEO data availability flags.

Sample records
35 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

Ready after review
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

No readiness blockers detected.

Next Steps

  • Verify the proposed sample assignments and case-versus-control comparison against the GEO metadata before using them in DESeq2 or another differential-expression tool.
  • Confirm processed count files and sample identifiers match the exported metadata.

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.

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

  • Assay differs from search intent Microarray Search intent expects bulk RNA-seq. Assay came from Normalization rules.
  • Disease context Crohn's disease, inflammatory bowel disease Disease context came from Normalization rules.
  • Likely case group Crohn's disease 6 samples
  • Likely control group Healthy control 29 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: 0%.
  • Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease.
  • Processed data is available for downstream review.

Cautions

  • Downgraded for tissue search because it is a biofluid cohort.
  • Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
  • Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
  • Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Normalized Fields

110 fields

Sample Group Preview

35 rows shown Show Hide
Study totals: Case 6 | Control 29 | Unassigned 0 | Excluded 0 | Ambiguous 0 35 rows shown
Group Role Accession Title Source / characteristics Reason
Crohn's disease Case GSM591109 CD25+ CP MCa Blood Disease state: Active Crohn's disease; Tissue: CD4+CD25+ T cells Case marker detected.
Crohn's disease Case GSM591110 CD25+ UW MCa Blood Disease state: Active Crohn's disease; Tissue: CD4+CD25+ T cells Case marker detected.
Crohn's disease Case GSM591111 CD25+ WR MCa Blood Disease state: Active Crohn's disease; Tissue: CD4+CD25+ T cells Case marker detected.
Crohn's disease Case GSM591112 CD25+ HD MCi Blood Disease state: Inactive Crohn's disease; Tissue: CD4+CD25+ T cells Case marker detected.
Crohn's disease Case GSM591113 CD25+ KP MCi Blood Disease state: Inactive Crohn's disease; Tissue: CD4+CD25+ T cells Case marker detected.
Crohn's disease Case GSM591114 CD25+ SN MCi Blood Disease state: Inactive Crohn's disease; Tissue: CD4+CD25+ T cells Case marker detected.
Healthy control Control GSM591080 CD25+ xyz C6 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591081 CD25+ xyz C4 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591082 CD25+ ukr C14 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591083 CD25+ ukr C12 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591084 CD25+ suk B50 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591085 CD25+ suk 69 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591086 CD25+ suk 68 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591087 CD25+ spf A34 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591088 CD25+ spf 82 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591089 CD25+ spf 81 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591090 CD25+ rog 54 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591091 CD25+ rog 53 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591092 CD25+ rog 52 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591093 CD25+ mpk B28 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591094 CD25+ mpk B27 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591095 CD25+ mpk B26 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591096 CD25+ lgrFCS A38 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591097 CD25+ lgrFCS 72 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591098 CD25+ lgrFCS 71 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591099 CD25+ khu 60 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591100 CD25+ khu 59 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591101 CD25+ ikr C2 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591102 CD25+ ikr C18 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591103 CD25+ ikr C1 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591104 CD25+ chu B2 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591105 CD25+ chu B16 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591106 CD25+ chu B1 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591107 CD25+ aje A12 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells Sample-local control marker detected.
Healthy control Control GSM591108 CD25+ aje A10 Blood Disease state: Normal; Tissue: CD4+CD25+ T cells 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.