organism: Homo sapiens
description: Protocols: Gastrointestinal tissue was collected as part of a surgical resection through the University of Michigan Tissue Procurement Core and was approved by the University of Michigan Medical School Institutional Review Board with informed consent obtained from the patient. Adenoma tissue, associated with invasive moderately differentiated colorectal adenocarcinoma, and histologically normal margin tissue were collected. Organoids were isolated from Matrigel droplets by mechanical disruption of the Matrigel with a 200 μL pipet tip in cold DPBS, rotated for 15 minutes at 4°C in 2 mM EDTA, and washed three times in cold DPBS with 3-minute centrifugations at 250xg, 4°C. DNA was extracted from tissue specimens first preserved in Allprotect Tissue Reagent (Qiagen, #76405) or directly from fresh colonoid preparations with the All prep DNA/RNA/protein mini kit (Qiagen, #80004). DNA was fragmented to 250bp using standard Covaris sonication. Fragmented DNA was prepared as a standard Illumina gDNAlibrary using IntegenX reagents. The samples were PCR amplified and the libraries were checked for quality and quantity.
attributes.tag: ENA first public
attributes.value: 2020-12-22
attributes.tag: ENA last update
attributes.value: 2020-12-18
attributes.tag: External Id
attributes.value: SAMEA7741265
attributes.tag: INSDC center alias
attributes.value: University of Michigan Medical School Department of Internal Medicine Division of Gastroenterology
attributes.tag: INSDC center name
attributes.value: University of Michigan Medical School Department of Internal Medicine Division of Gastroenterology
attributes.tag: INSDC first public
attributes.value: 2020-12-22T04:10:02Z
attributes.tag: INSDC last update
attributes.value: 2020-12-18T17:52:16Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-9936:40139_adenoma tumor tissue_time-0
attributes.tag: age
attributes.value: 46
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell line
attributes.value: 14-881 adenoma tissue
attributes.tag: common name
attributes.value: human
attributes.tag: developmental stage
attributes.value: adult
attributes.tag: disease
attributes.value: colorectal adenoma
attributes.tag: organism part
attributes.value: rectum
attributes.tag: sample name
attributes.value: E-MTAB-9936:40139_adenoma tumor tissue_time-0
attributes.tag: sex
attributes.value: male