MAGE-TAB Version 1.1 Investigation Title Expression profiling of budding cells in colorectal cancer suggests an EMT-like phenotype and molecular subtype switching Experimental Design development or differentiation design Experimental Design Term Source REF EFO Experimental Design Term Accession Number EFO_0001746 Experimental Factor Name developmental stage Experimental Factor Type developmental stage Experimental Factor Term Source REF EFO Experimental Factor Term Accession Number EFO_0000399 Person Last Name Boeckx Person First Name Bram Person Mid Initials Person Email bram.boeckx@vib-kuleuven.be Person Phone Person Fax Person Affiliation Laboratory of translational genetics Vesalius research center, VIB Department of Oncology, KU Leuven Person Address Herestraat 49, box 0912 O&N4, bldg 404-24 3000 Leuven Belgium Person Roles submitter Person Roles Term Source REF Person Roles Term Accession Number Quality Control Type Quality Control Term Source REF Quality Control Term Accession Number Replicate Type Replicate Term Source REF Replicate Term Accession Number Normalization Type Normalization Term Source REF Normalization Term Accession Number Date of Experiment 2015-09-21 Public Release Date 2017-02-04 PubMed ID Publication DOI Publication Author List Linde De Smedt, Sofie Palmans, Matthieu Moisse, Bram Boeckx, Dominiek Smeets, Olivier Govaere, Jasper Wouters, Jeroen Dekervel, Daan Andel, Thomas Tousseyn, Gert De Hertogh, Sabine Tejpar, Diether Lambrechts, Xavier Sagaert Publication Title Expression profiling of budding cells in colorectal cancer suggests an EMT-like phenotype and molecular subtype switching Publication Status in preparation Publication Status Term Source REF Publication Status Term Accession Number Experiment Description Tumour buds undergo phenotype switching while detaching from the main tumour, as they acquire more migratory characteristics and tend to stop proliferating. Simultaneously, an EMT-like signature is observed in the tumour buds under the form of active WNT, TGF and receptor tyrosine kinase signalling. In addition, FOXA2 and RUNX2 well known transcription factors in other cancer types were also differentially expressed in the buds compared to the main tumour mass, hinting at the potential role in tumour budding and initiation of metastasis in colorectal cancer. Protocol Name P-MTAB-47440 P-MTAB-47441 P-MTAB-47442 Protocol Type sample collection protocol nucleic acid library construction protocol nucleic acid sequencing protocol Protocol Term Source REF EFO EFO EFO Protocol Term Accession Number EFO_0005518 EFO_0004184 EFO_0004170 Protocol Description 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. The libraries were sequenced on a HiSeq2500 (Illumina) using a V4 flowcell generating 1 x 50 bp reads. Protocol Parameters Protocol Hardware Illumina HiSeq 2500 Protocol Software Protocol Contact Term Source Name EFO ArrayExpress Term Source File http://www.ebi.ac.uk/efo/ http://www.ebi.ac.uk/arrayexpress/ Term Source Version 2.38 SDRF File E-MTAB-4065.sdrf.txt Comment [Submitted Name] Expression profiling of budding cells in colorectal cancer suggests an EMT-like phenotype and molecular subtype switching Comment [SecondaryAccession] ERP013215 Comment [SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/ERR1141826-ERR1141841 Comment [AEExperimentType] RNA-seq of coding RNA Comment[ArrayExpressAccession] E-MTAB-4065 Comment [AEMINSEQEScore] 3