UC inflamed
Homo sapiens
Protocols: Pinch biopsies were obtained during routine colonoscopies from one patient with ulcerative colitis (1x inflamed and 1x noninflamed region) and one patient with primary sclerosing cholangitis concomitant with colitis (noninflamed region only). Biopsies were embedded in optimal cutting temperature medium and fresh-frozen on dry ice.  All samples were sectioned using the Leica CM1860 UV cryostat and two to three serial cuts were included on each Stereo-seq slide. Tissue sections were adhered to the Stereo-seq chip and incubated in -20°C methanol for 30 minutes. Stereo-seq slides were fluorescently stained with Qubit ssDNA Assay Kit (Q10212; ThermoFisher) as per the manual and imaged using a Leica DM6 microscope with a CTR6 LED electronics box. The Stereo-seq Permeabilisation Set for Chip-on-a-slide user manual (version B) was followed to obtain an optimal permeabilisation time for colonic mucosa tissue of 8 minutes.  The cDNA was purified using SPRIselect Beads (B23318; Beckman Coulter). cDNA quality was quantified before and following cDNA library preparation using Qubit 4 fluorometer with Qubit dsDNA mix (Q33230; Invitrogen) and Agilent Tapestation High Sensitivity D5000 ScreenTape Assay (5067-5592 & 5067-5593; Agilent Technologies).
ENA first public
2026-06-12
INSDC center name
Garvan
INSDC status
public
Submitter Id
E-MTAB-17162:UC inflamed
age
41
broker name
ArrayExpress
collection date
not collected
common name
human
developmental stage
adult
disease
ulcerative colitis
geographic location (country and/or sea)
not collected
individual
UC-11
isolate
not applicable
organism part
rectum
sample name
E-MTAB-17162:UC inflamed
scientific_name
Homo sapiens
sex
male