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

employing RNA sequencing (RNAseq) to analyze transcriptomic changes in mucosal biopsy specimens

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The cDNA library was constructed with 1.0 μg of total RNA using NEBNext Ultra II directional RNA library prep kit for Illumina sequencer.

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"instrument_model": {"Illumina HiSeq 2500": 45}

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Assembly: GRCh37

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We compare active (UCA) and macroscopically inactive (UCI) inflammatory areas during colonoscopy in UC patients with normal controls (NC).

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we obtained RNAseq data from 15 NCs

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Public on Mar 19 2024

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GSE243625_RNAseq_colon.txt.gz

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

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RNA quality was assessed by RIN (RNA Integrity Number) algorithm on the Agilent 2100 bioanalyzer.

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mucosal biopsy specimens

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"Active ulceraitve colitis": 15

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"sample_count": 45

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Colonoscopic biopsy specimens

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