title: SAG046_Main
organism: Homo sapiens
description: Protocols: Eight cases of colorectal cancer were selected from the archive of the pathology department of the University Hospitals of Leuven (Belgium). Inclusion criteria were: (1) diagnosis of colorectal cancer was established according to the criteria of the World Health Organisation (WHO) (2) diagnosis was made between 2003 and 2012 (3) patients were free from pre-operative radio or chemotherapy to avoid interference with the grade of tumour budding and gene expression profile (4) availability of FFPE material (5) availability of matched fresh frozen (FF) tissue (6) high tumour budding was observed in both FFPE and FF tissue at the invasive margin of the tumour (7) good or moderate (non-mucinous) differentiation pattern. RNA sequencing was performed on 8 budding and 8 matched main tumors using the TruSeq RNA access Library Prep Kit (Illumina) following to the manufacturers instructions. In short, RNA is fragmented using divalent cations at 94oC for 8 minutes. The cleaved RNA fragments are then converted to cDNA using random priming during first and second strand synthesis. An A-base is then added to the resulting double-stranded cDNA fragments and sequencing adapters are ligated. The resulting library is amplified using PCR. Subsequently, 2 rounds of 90 minutes hybridization at 58oC with sequence-specific probes were used to capture the coding regions of the transcriptome and bind them to streptavidin magnetic beads. Two heated washes remove non-specificly bound fragments from the beads after which the captured fragments are again enriched with PCR.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2017-02-04T17:03:05Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2018-03-09T09:26:56Z
attributes.tag: External Id
attributes.value: SAMEA3670457
attributes.tag: INSDC center name
attributes.value: Laboratory of translational genetics Vesalius research center, VIB Department of Oncology, KU Leuven
attributes.tag: INSDC first public
attributes.value: 2017-02-04T17:03:05Z
attributes.tag: INSDC last update
attributes.value: 2018-03-09T09:26:56Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-4065:SAG046_Main
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell type
attributes.value: colorectal cancer cell
attributes.tag: common name
attributes.value: human
attributes.tag: developmental stage
attributes.value: main cell
attributes.tag: disease
attributes.value: colorectal cancer
attributes.tag: sample name
attributes.value: E-MTAB-4065:SAG046_Main
attributes.tag: scientific_name
attributes.value: Homo sapiens