title: Sample 4
organism: Homo sapiens
description: Protocols: Biopsy was obtained from the patient under informed consent in DMEM F12 containing 10% FBS and 2% P/S and processed within 2 hours. The tissue was minced into small pieces and washed extensively with PBS before being dissociated with collagenase IV for 2-3 hours and additional 15' with TripLE at 37C. Digestion was stopped by medium dilution and the pellet was resuspended in 70% Matrigel. Organoids were cultured in endometrial cancer organoids culture medium. organoids were cultured embedded in 70% Matrigel in 48-wells low attachment culture plates in endometrial cancer organoid culture medium which was refreshed every 2 days. Organoids were enzymatically and mechanically passaged with TripLE every 2 weeks. In order to be passaged, organoids were removed from Matrigel with ice-cold DMEM F12 and centrifuge at 230g for 5'. The pellet was resuspended in 500ul of TripLE and incubated for 10' at 37C. Incubation was stopped by dilution and organoids were mechanically tritured before being centrifuged at 230g for 5'. Finally, the pellet was resuspended in 70% Matrigel and cells were seeded. Matrigel was allowed to solidify and 250ul of pre-warmed medium was added thereafter. Organoids were split at 1/4 to 1/10 ratio. Organoids with low passage numbers were used for this experiments unless otherwise stated. Organoids were recovered from Matrigel with ice-cold DMEM F12 and centrifuged at 230g for 5'. The pellet was resuspended in 200ul of PBS and genomic DNA was isolated using the Purelink Genomic Mini Kit (Invitrogen) according to the manufacturer's instructions. DNA concentration was measured with a nanodrop and DNA was stored at -80C before being processed for exome sequencing. Whole genome DNA libraries were created using the Illumina TruSeq DNA sample preparation kit V2 according to the manufacturer's instructions.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2019-06-04T17:04:07Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2019-02-14T17:39:45Z
attributes.tag: External Id
attributes.value: SAMEA5340608
attributes.tag: INSDC center name
attributes.value: VIB Center for Cancer Biology (CCB) Laboratory for Translational Genetics Department of Human Genetics KULeuven
attributes.tag: INSDC first public
attributes.value: 2019-06-04T17:04:07Z
attributes.tag: INSDC last update
attributes.value: 2019-02-14T17:39:45Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-7687:Sample 4
attributes.tag: age
attributes.value: not available
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: common name
attributes.value: human
attributes.tag: developmental stage
attributes.value: adult
attributes.tag: disease
attributes.value: Endometrial cancer
attributes.tag: disease staging
attributes.value: I
attributes.tag: growth condition
attributes.value: organoid culture
attributes.tag: individual
attributes.value: 2
attributes.tag: organism part
attributes.value: endometrium
attributes.tag: sample name
attributes.value: E-MTAB-7687:Sample 4
attributes.tag: scientific_name
attributes.value: Homo sapiens
attributes.tag: sex
attributes.value: female
attributes.tag: time
attributes.value: passage 9
attributes.tag: tumor grading
attributes.value: IB