GSE83381

Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis [RNA-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

10 case / 0 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: Homo sapiens
Whole-study samples: 20 samples
Specimen: Biofluid
Reported/interpreted study design: Treatment vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Mehta S, Pantano L, Sui SH, Jeffrey KL
Contact name: Lorena Pantano
Submission date: 2016-06-15
Last update: 2019-05-15
Organization: Harvard Chan School of Public Health
Department: Biostatistics
Public date: 2017-05-03
Experiment types: Expression profiling by high throughput sequencing
Platforms: GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Series type: SubSeries
SubSeries: Not available
BioProject: PRJNA325740

Summary

Introduction: SP140 is a bromodomain/plant homeo domain (PHD)-containing reader with immune-restricted expression, and single nucleotide polymorphisms (SNPs) within SP140 associate with Crohn’s disease (CD). However, the function of SP140 and the consequences of disease-associated SP140 SNPs have remained unknown. Results: Individuals carrying CD-associated SNPs within SP140 had defective SP140 mRNA splicing, diminished SP140 protein, and severely suppressed innate immune signatures that stratified them from other CD patients. Conclusion: SP140 is a critical orchestrator of macrophage identity, and a loss of SP140 due to genetic variation contributes to a molecularly defined subset of CD characterized by suppressed innate immunity.

Overall design

RNA-seq of 8 samples of peripheral blood derived mononuclear cells from CD patients having T/T or C/C genotype for rs6716753 SNP, with and without LPS treatment. 4 samples from healthy individuals with and without LPS treatment. RNA-seq of human macrophages (total 8 samples from 2 independent donors) stimulated with IFNg for 24h, and LPS (100ng/mL) for 4 hours: siRNA mediated knockdown of SP140 versus controls. RNA-seq of human macrophages (total 8 samples from 2 independent donors) stimulated with IFNg for 24h, and LPS (100ng/mL) for 4 hours for each condition: siRNA mediated knockdown of SP140 versus controls.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 20 GSM samples	Primary source
recount3	Trusted source evidence for processed count availability. recount3 project ID srp076599	Available
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

85% 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

3/15 pts

Unassigned or review-needed samples remain before analysis.

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

4 samples are still unassigned.
8 samples need manual grouping review.

Next Steps

Resolve unassigned or review-needed samples in the grouping table.

Analysis Preparation Checklist

4/6 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

Needs review

8 review-needed samples and 4 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

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.

One or more samples are unassigned and need manual grouping decisions.

One or more samples were flagged for manual review.

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

Disease context Crohn's disease Disease context came from Normalization rules.
Likely case group Crohn's disease 12 samples
Likely control group Control 4 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: Treatment vs control. Specimen: Biofluid. Comparison suitability: 0%.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Crohn's disease.
Processed data is available for downstream review.
External evidence: recount3 reports trusted processed count availability.

Cautions

Downgraded for tissue search because it is a biofluid cohort.
Downgraded for tissue search because it is a treatment/control experiment.
Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons.
Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
Overall score capped because comparison suitability is weak for the selected search intent.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Ambiguous sample metadata was detected in 8 sample(s): GSM2344751 matched "disease status: unknown"; GSM2344752 matched "disease status: unknown"; GSM2344753 matched "disease status: unknown"; additional ambiguous samples omitted. Review these samples before inclusion or manual group assignment.
Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.

Normalized Fields

69 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source blood GSM2200449 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood derived mononuclear cells sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2200450 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood derived mononuclear cells sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2200451 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood derived mononuclear cells sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2200452 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood derived mononuclear cells sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2200453 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood derived mononuclear cells sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2200454 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood derived mononuclear cells sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2200455 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood derived mononuclear cells sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2200456 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood derived mononuclear cells sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2200457 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood derived mononuclear cells sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2200458 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood derived mononuclear cells sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2200459 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood derived mononuclear cells sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2200460 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood derived mononuclear cells sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2344751 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2344752 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2344753 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2344754 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2344755 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2344756 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2344757 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2344758 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood sample-anatomical-source-v1 sample-local anatomical source

assay_type bulk RNA-seq GSE83381 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence bulk rna-seq dataset_accession: GSE83381 dataset_title: Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis [RNA-... keyword match keyword match: bulk rna-seq

cell_population peripheral blood mononuclear cells GSM2344751 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Donor 1 control 0h Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: none controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2344752 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Donor 1 SP140 KD 0h Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: SP140 controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2344753 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Donor 1 control 4h LPS Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: none controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2344754 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Donor 1 SP140 KD 4h LPS Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: SP140 controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2344755 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Donor 2 control 0h Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: none controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2344756 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Donor 2 SP140 KD 0h Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: SP140 controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2344757 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Donor 2 control 4h LPS Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: none controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM2344758 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Donor 2 SP140 KD 4h LPS Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: SP140 controlled vocabulary controlled vocabulary cell population match: pbmc

disease Crohn's disease GSE83381 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease dataset_accession: GSE83381 dataset_title: Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis [RNA-... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2200449 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD T/T rep1 Peripheral blood derived mononuclear cells disease state: Crohn's disease; cell type: Peripheral blood derived mononuclear cells; genotype: T/T rs6716753 controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2200450 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD C/C rep1 Peripheral blood derived mononuclear cells disease state: Crohn's disease; cell type: Peripheral blood derived mononuclear cells; genotype: C/C rs6716753 controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2200451 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD T/T rep2 Peripheral blood derived mononuclear cells disease state: Crohn's disease; cell type: Peripheral blood derived mononuclear cells; genotype: T/T rs6716753 controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2200452 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD C/C rep2 Peripheral blood derived mononuclear cells disease state: Crohn's disease; cell type: Peripheral blood derived mononuclear cells; genotype: C/C rs6716753 controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2200453 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD T/T LPS+ rep1 Peripheral blood derived mononuclear cells disease state: Crohn's disease; cell type: Peripheral blood derived mononuclear cells; genotype: T/T rs6716753 controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2200454 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD C/C LPS+ rep1 Peripheral blood derived mononuclear cells disease state: Crohn's disease; cell type: Peripheral blood derived mononuclear cells; genotype: C/C rs6716753 controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2200455 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD T/T LPS+ rep2 Peripheral blood derived mononuclear cells disease state: Crohn's disease; cell type: Peripheral blood derived mononuclear cells; genotype: T/T rs6716753 controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2200456 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD C/C LPS+ rep2 Peripheral blood derived mononuclear cells disease state: Crohn's disease; cell type: Peripheral blood derived mononuclear cells; genotype: C/C rs6716753 controlled vocabulary controlled vocabulary disease match: Crohn's disease

organism Homo sapiens GSE83381 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE83381 dataset_title: Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis [RNA-... keyword match keyword match: homo sapiens

specimen_material PBMC preparation GSM2344751 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Donor 1 control 0h Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: none controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2344752 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Donor 1 SP140 KD 0h Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: SP140 controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2344753 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Donor 1 control 4h LPS Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: none controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2344754 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Donor 1 SP140 KD 4h LPS Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: SP140 controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2344755 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Donor 2 control 0h Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: none controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2344756 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Donor 2 SP140 KD 0h Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: SP140 controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2344757 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Donor 2 control 4h LPS Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: none controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM2344758 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc Donor 2 SP140 KD 4h LPS Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: SP140 controlled vocabulary controlled vocabulary specimen material match: pbmc

tissue blood GSE83381 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood dataset_accession: GSE83381 dataset_title: Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis [RNA-... controlled vocabulary controlled vocabulary tissue match: blood

tissue intestine GSE83381 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal dataset_accession: GSE83381 dataset_title: Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis [RNA-... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue blood GSM2200449 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood CD T/T rep1 Peripheral blood derived mononuclear cells disease state: Crohn's disease; cell type: Peripheral blood derived mononuclear cells; genotype: T/T rs6716753 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2200450 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood CD C/C rep1 Peripheral blood derived mononuclear cells disease state: Crohn's disease; cell type: Peripheral blood derived mononuclear cells; genotype: C/C rs6716753 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2200451 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood CD T/T rep2 Peripheral blood derived mononuclear cells disease state: Crohn's disease; cell type: Peripheral blood derived mononuclear cells; genotype: T/T rs6716753 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2200452 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood CD C/C rep2 Peripheral blood derived mononuclear cells disease state: Crohn's disease; cell type: Peripheral blood derived mononuclear cells; genotype: C/C rs6716753 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2200453 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood CD T/T LPS+ rep1 Peripheral blood derived mononuclear cells disease state: Crohn's disease; cell type: Peripheral blood derived mononuclear cells; genotype: T/T rs6716753 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2200454 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood CD C/C LPS+ rep1 Peripheral blood derived mononuclear cells disease state: Crohn's disease; cell type: Peripheral blood derived mononuclear cells; genotype: C/C rs6716753 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2200455 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood CD T/T LPS+ rep2 Peripheral blood derived mononuclear cells disease state: Crohn's disease; cell type: Peripheral blood derived mononuclear cells; genotype: T/T rs6716753 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2200456 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood CD C/C LPS+ rep2 Peripheral blood derived mononuclear cells disease state: Crohn's disease; cell type: Peripheral blood derived mononuclear cells; genotype: C/C rs6716753 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2200457 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood WT C/C rep1 Peripheral blood derived mononuclear cells disease state: non-disease; cell type: Peripheral blood derived mononuclear cells; genotype: C/C rs6716753 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2200458 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood WT C/C rep2 Peripheral blood derived mononuclear cells disease state: non-disease; cell type: Peripheral blood derived mononuclear cells; genotype: C/C rs6716753 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2200459 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood WT C/C LPS rep1 Peripheral blood derived mononuclear cells disease state: non-disease; cell type: Peripheral blood derived mononuclear cells; genotype: C/C rs6716753 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2200460 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood WT C/C LPS rep2 Peripheral blood derived mononuclear cells disease state: non-disease; cell type: Peripheral blood derived mononuclear cells; genotype: C/C rs6716753 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2344751 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Donor 1 control 0h Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: none controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2344752 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Donor 1 SP140 KD 0h Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: SP140 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2344753 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Donor 1 control 4h LPS Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: none controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2344754 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Donor 1 SP140 KD 4h LPS Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: SP140 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2344755 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Donor 2 control 0h Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: none controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2344756 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Donor 2 SP140 KD 0h Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: SP140 controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2344757 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Donor 2 control 4h LPS Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: none controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2344758 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood Donor 2 SP140 KD 4h LPS Peripheral blood disease status: unknown; cell type: PBMC derived macrophage; sirna: SP140 controlled vocabulary controlled vocabulary tissue match: blood

Sample Group Preview

20 rows shown Show Hide

Study totals: Case 10 | Control 0 | Unassigned 2 | Excluded 0 | Ambiguous 8 20 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Crohn's disease	Case	GSM2200449	CD T/T rep1	Peripheral blood derived mononuclear cells Disease state: Crohn's disease; Cell type: Peripheral blood derived mononuclear cells; Genotype: T/T rs6716753	Case marker detected.
Crohn's disease	Case	GSM2200450	CD C/C rep1	Peripheral blood derived mononuclear cells Disease state: Crohn's disease; Cell type: Peripheral blood derived mononuclear cells; Genotype: C/C rs6716753	Case marker detected.
Crohn's disease	Case	GSM2200451	CD T/T rep2	Peripheral blood derived mononuclear cells Disease state: Crohn's disease; Cell type: Peripheral blood derived mononuclear cells; Genotype: T/T rs6716753	Case marker detected.
Crohn's disease	Case	GSM2200452	CD C/C rep2	Peripheral blood derived mononuclear cells Disease state: Crohn's disease; Cell type: Peripheral blood derived mononuclear cells; Genotype: C/C rs6716753	Case marker detected.
Crohn's disease	Case	GSM2200453	CD T/T LPS+ rep1	Peripheral blood derived mononuclear cells Disease state: Crohn's disease; Cell type: Peripheral blood derived mononuclear cells; Genotype: T/T rs6716753	Case marker detected.
Crohn's disease	Case	GSM2200454	CD C/C LPS+ rep1	Peripheral blood derived mononuclear cells Disease state: Crohn's disease; Cell type: Peripheral blood derived mononuclear cells; Genotype: C/C rs6716753	Case marker detected.
Crohn's disease	Case	GSM2200455	CD T/T LPS+ rep2	Peripheral blood derived mononuclear cells Disease state: Crohn's disease; Cell type: Peripheral blood derived mononuclear cells; Genotype: T/T rs6716753	Case marker detected.
Crohn's disease	Case	GSM2200456	CD C/C LPS+ rep2	Peripheral blood derived mononuclear cells Disease state: Crohn's disease; Cell type: Peripheral blood derived mononuclear cells; Genotype: C/C rs6716753	Case marker detected.
Treated	Case	GSM2200459	WT C/C LPS rep1	Peripheral blood derived mononuclear cells Disease state: Non-disease; Cell type: Peripheral blood derived mononuclear cells; Genotype: C/C rs6716753	Treatment case marker detected.
Treated	Case	GSM2200460	WT C/C LPS rep2	Peripheral blood derived mononuclear cells Disease state: Non-disease; Cell type: Peripheral blood derived mononuclear cells; Genotype: C/C rs6716753	Treatment case marker detected.
Unassigned	Unassigned	GSM2200457	WT C/C rep1	Peripheral blood derived mononuclear cells Disease state: Non-disease; Cell type: Peripheral blood derived mononuclear cells; Genotype: C/C rs6716753	No explicit case or control marker detected.
Unassigned	Unassigned	GSM2200458	WT C/C rep2	Peripheral blood derived mononuclear cells Disease state: Non-disease; Cell type: Peripheral blood derived mononuclear cells; Genotype: C/C rs6716753	No explicit case or control marker detected.
Control	Ambiguous	GSM2344751	Donor 1 control 0h	Peripheral blood Disease status: Unknown; Cell type: PBMC derived macrophage; Sirna: None	ambiguous sample: Ambiguous case/control metadata detected.
Unassigned	Ambiguous	GSM2344752	Donor 1 SP140 KD 0h	Peripheral blood Disease status: Unknown; Cell type: PBMC derived macrophage; Sirna: SP140	ambiguous sample: Ambiguous case/control metadata detected.
Control	Ambiguous	GSM2344753	Donor 1 control 4h LPS	Peripheral blood Disease status: Unknown; Cell type: PBMC derived macrophage; Sirna: None	ambiguous sample: Ambiguous case/control metadata detected.
Treated	Ambiguous	GSM2344754	Donor 1 SP140 KD 4h LPS	Peripheral blood Disease status: Unknown; Cell type: PBMC derived macrophage; Sirna: SP140	ambiguous sample: Ambiguous case/control metadata detected.
Control	Ambiguous	GSM2344755	Donor 2 control 0h	Peripheral blood Disease status: Unknown; Cell type: PBMC derived macrophage; Sirna: None	ambiguous sample: Ambiguous case/control metadata detected.
Unassigned	Ambiguous	GSM2344756	Donor 2 SP140 KD 0h	Peripheral blood Disease status: Unknown; Cell type: PBMC derived macrophage; Sirna: SP140	ambiguous sample: Ambiguous case/control metadata detected.
Control	Ambiguous	GSM2344757	Donor 2 control 4h LPS	Peripheral blood Disease status: Unknown; Cell type: PBMC derived macrophage; Sirna: None	ambiguous sample: Ambiguous case/control metadata detected.
Treated	Ambiguous	GSM2344758	Donor 2 SP140 KD 4h LPS	Peripheral blood Disease status: Unknown; Cell type: PBMC derived macrophage; Sirna: SP140	ambiguous sample: Ambiguous case/control metadata 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.