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← IBD single-cell transcriptomics

Inflammatory transcriptomic signatures and cell type compositions in inflamed and non-inflamed colonic mucosa of ulcerative colitis

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Dataset overview

Participants None
Samples 45
Reuse readiness 4.9/10 evidence-backed score

Inflammatory transcriptomic signatures and cell type compositions in inflamed and non-inflamed colonic mucosa of ulcerative colitis.

Song EM, Saqib J, Joo YH, Ramsha Z, Moon CM, Jung SA, Kim J. · Genes & diseases · 2024

doi:10.1016/j.gendis.2024.101447 ↗ PMID 39926325 ↗ PMC11804533 ↗

Study facts

Organism
Homo sapiens
Platform
Illumina NovaSeq 6000
Age group
—
Disease groups
—
Anatomical sites
colon

Data availability

  • Processed matrix

File types TXT

Strengths & limitations for reuse

Strengths

  • Processed matrices are advertised

Limitations

  • Not documented: raw counts are advertised
  • Not documented: cell metadata are advertised
  • Not documented: participant counts are documented
Extraction evidence & provenance

Each extracted field is shown with the source excerpt and location used to resolve it.

Assay

FieldValueEvidence
assay.assay_type bulk RNA sequencing
This integrative approach using bulk and single cell transcriptomics

Section series, offset —
assay.library_chemistry NEBNext Ultra II directional RNA library prep kit
The cDNA library was constructed with 1.0 μg of total RNA using NEBNext Ultra II directional RNA library prep kit for Illumina sequencer.

Section samples, offset —
assay.platform Illumina NovaSeq 6000
100bp paired-end sequencing reads were obtained using Illumina NovaSeq 6000.

Section samples, offset —
assay.reference_genome GRCh37
Assembly: GRCh37

Section samples, offset —

Data_Assets

FieldValueEvidence
data_assets.open_access True
Public on Mar 19 2024

Section series, offset —
data_assets.processed_matrix True inferred
GSE243625_RNAseq_colon.txt.gz

Section —, offset —

Processing

FieldValueEvidence
processing.normalization_method FPKM
we computed Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using Cufflinks.

Section samples, offset —
processing.quality_control_reported True
RNA quality was assessed by RIN (RNA Integrity Number) algorithm on the Agilent 2100 bioanalyzer.

Section samples, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['colon']
15 colonic tissue samples from UCI, and 15 from UCA

Section —, offset —
specimens.inflamed_status_available True
15 active (inflamed), 15 inactive (non-inflamed) samples of ulcerative colitis

Section series, offset —
specimens.number_of_samples 45
"n_samples": 45

Section geo_record_summary, offset —