WUCA-CD-36
Homo sapiens
Protocols: We retrospectively obtained de-identified FFPE tissue from patients who underwent ileo-colic resection surgery at Barnes-Jewish Hospital, St. Louis between 2005 and 2010. CD patient surgical resections were due to complications associated with the disease, whereas control resections were due to adenoma, carcinoma or abdominal trauma. The set of hematoxylin and eosin-stained tissue sections from each resection were obtained and examined by two pathologists (T.C.L. and T.S.S.) to identify the uninvolved proximal margin (terminal ileum) of each resection. These tissue sections were then further evaluated to identify those that met the histological inclusion criteria for this study. The criteria were that the sample had at least 100 well-oriented intestinal crypts (contained crypt lumens that extended from the apex to the base of the crypt) and absent/minimal active or chronic inflammatory disease (e.g., cryptitis, crypt abscess, architectural distortion, pyloric gland metaplasia, etc.).The study protocol was approved by the Institutional Review Board of Washington University. Patients were recruited by the Washington University Digestive Diseases Research Core Center (DDRCC). Written informed consent was obtained from all study participants prior to inclusion in the study. For samples that met the histological inclusion criteria, two fresh, unstained 5-µm FFPE tissue sections on glass microscope slides were obtained. Slides were not baked after cutting. For each sample, the two tissue sections were scraped off of the slides using a clean razor and placed in 1.5 mL Eppendorf tubes. The tubes were briefly centrifuged to place the sample towards the bottoms or sides of the tube. RNA extraction and DNase treatment was performed using the RNeasy FFPE kit (Qiagen) according to the manufacturer's instructions, using the Xylene protocol for the paraffin removal step and 30 µL RNase-free H2O for the elution step. RNA was initially quantified by NanoDrop. Subsequent total RNA quantification and quality assessment was performed by Bioanalyzer 2100 (Agilent Technologies). Samples were excluded from the study if >20% of the RNA fragments were >200 base pairs in length, as determined with the Bioanalyzer software. Library preparation was performed by the Genome Technology Access Center (GTAC) at Washington University. Library preparation used 150 ng of total RNA. ds-cDNA was generated using the Ovation RNA-seq FFPE system (Nugen, per manufacturer's instructions). cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags.
ENA first public
2018-01-01
ENA last update
2017-05-26
External Id
SAMEA104101938
INSDC center alias
Washington University School of Medicine
INSDC center name
Washington University School of Medicine
INSDC first public
2018-01-01T17:01:40Z
INSDC last update
2017-05-26T09:34:23Z
INSDC status
public
Submitter Id
E-MTAB-5783:WUCA-CD-36
broker name
ArrayExpress
common name
human
disease
Crohn's disease
organism part
small intestine
sample name
E-MTAB-5783:WUCA-CD-36
sampling site
terminal ileum
specimen with known storage state
paraffin specimen