ERX1220675 E-MTAB-4065:SAG031_Main E-MTAB-4065:SAG031_Main ERP013215 E-MTAB-4065 Expression profiling of budding cells in colorectal cancer suggests an EMT-like phenotype and molecular subtype switching ERS977602 SAMEA3670453 E-MTAB-4065:SAG031_Main SAG031_Main RNA-Seq TRANSCRIPTOMIC Hybrid Selection 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. Illumina HiSeq 2500 Experimental Factor: main cell developmental stage ERX1220676 E-MTAB-4065:SAG034_Bud E-MTAB-4065:SAG034_Bud ERP013215 E-MTAB-4065 Expression profiling of budding cells in colorectal cancer suggests an EMT-like phenotype and molecular subtype switching ERS977603 SAMEA3670454 E-MTAB-4065:SAG034_Bud SAG034_Bud RNA-Seq TRANSCRIPTOMIC Hybrid Selection 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. Illumina HiSeq 2500 Experimental Factor: bud cell developmental stage ERX1220677 E-MTAB-4065:SAG037_Main E-MTAB-4065:SAG037_Main ERP013215 E-MTAB-4065 Expression profiling of budding cells in colorectal cancer suggests an EMT-like phenotype and molecular subtype switching ERS977604 SAMEA3670455 E-MTAB-4065:SAG037_Main SAG037_Main RNA-Seq TRANSCRIPTOMIC Hybrid Selection 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. Illumina HiSeq 2500 Experimental Factor: main cell developmental stage ERX1220678 E-MTAB-4065:SAG039_Bud E-MTAB-4065:SAG039_Bud ERP013215 E-MTAB-4065 Expression profiling of budding cells in colorectal cancer suggests an EMT-like phenotype and molecular subtype switching ERS977605 SAMEA3670456 E-MTAB-4065:SAG039_Bud SAG039_Bud RNA-Seq TRANSCRIPTOMIC Hybrid Selection 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. Illumina HiSeq 2500 Experimental Factor: bud cell developmental stage ERX1220679 E-MTAB-4065:SAG046_Main E-MTAB-4065:SAG046_Main ERP013215 E-MTAB-4065 Expression profiling of budding cells in colorectal cancer suggests an EMT-like phenotype and molecular subtype switching ERS977606 SAMEA3670457 E-MTAB-4065:SAG046_Main SAG046_Main RNA-Seq TRANSCRIPTOMIC Hybrid Selection 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. Illumina HiSeq 2500 Experimental Factor: main cell developmental stage ERX1220680 E-MTAB-4065:SAG049_Bud E-MTAB-4065:SAG049_Bud ERP013215 E-MTAB-4065 Expression profiling of budding cells in colorectal cancer suggests an EMT-like phenotype and molecular subtype switching ERS977607 SAMEA3670458 E-MTAB-4065:SAG049_Bud SAG049_Bud RNA-Seq TRANSCRIPTOMIC Hybrid Selection 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. Illumina HiSeq 2500 Experimental Factor: bud cell developmental stage ERX1220681 E-MTAB-4065:SAG050_Main E-MTAB-4065:SAG050_Main ERP013215 E-MTAB-4065 Expression profiling of budding cells in colorectal cancer suggests an EMT-like phenotype and molecular subtype switching ERS977608 SAMEA3670459 E-MTAB-4065:SAG050_Main SAG050_Main RNA-Seq TRANSCRIPTOMIC Hybrid Selection 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. Illumina HiSeq 2500 Experimental Factor: main cell developmental stage ERX1220682 E-MTAB-4065:SAG052_Bud E-MTAB-4065:SAG052_Bud ERP013215 E-MTAB-4065 Expression profiling of budding cells in colorectal cancer suggests an EMT-like phenotype and molecular subtype switching ERS977609 SAMEA3670460 E-MTAB-4065:SAG052_Bud SAG052_Bud RNA-Seq TRANSCRIPTOMIC Hybrid Selection 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. Illumina HiSeq 2500 Experimental Factor: bud cell developmental stage ERX1220683 E-MTAB-4065:SAG062_Main E-MTAB-4065:SAG062_Main ERP013215 E-MTAB-4065 Expression profiling of budding cells in colorectal cancer suggests an EMT-like phenotype and molecular subtype switching ERS977610 SAMEA3670461 E-MTAB-4065:SAG062_Main SAG062_Main RNA-Seq TRANSCRIPTOMIC Hybrid Selection 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. Illumina HiSeq 2500 Experimental Factor: main cell developmental stage ERX1220684 E-MTAB-4065:SAG064_Bud E-MTAB-4065:SAG064_Bud ERP013215 E-MTAB-4065 Expression profiling of budding cells in colorectal cancer suggests an EMT-like phenotype and molecular subtype switching ERS977611 SAMEA3670462 E-MTAB-4065:SAG064_Bud SAG064_Bud RNA-Seq TRANSCRIPTOMIC Hybrid Selection 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. Illumina HiSeq 2500 Experimental Factor: bud cell developmental stage ERX1220685 E-MTAB-4065:SAG068_Main E-MTAB-4065:SAG068_Main ERP013215 E-MTAB-4065 Expression profiling of budding cells in colorectal cancer suggests an EMT-like phenotype and molecular subtype switching ERS977612 SAMEA3670463 E-MTAB-4065:SAG068_Main SAG068_Main RNA-Seq TRANSCRIPTOMIC Hybrid Selection 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. Illumina HiSeq 2500 Experimental Factor: main cell developmental stage ERX1220686 E-MTAB-4065:SAG071_Bud E-MTAB-4065:SAG071_Bud ERP013215 E-MTAB-4065 Expression profiling of budding cells in colorectal cancer suggests an EMT-like phenotype and molecular subtype switching ERS977613 SAMEA3670464 E-MTAB-4065:SAG071_Bud SAG071_Bud RNA-Seq TRANSCRIPTOMIC Hybrid Selection 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. Illumina HiSeq 2500 Experimental Factor: bud cell developmental stage ERX1220687 E-MTAB-4065:SAG075_Main E-MTAB-4065:SAG075_Main ERP013215 E-MTAB-4065 Expression profiling of budding cells in colorectal cancer suggests an EMT-like phenotype and molecular subtype switching ERS977614 SAMEA3670465 E-MTAB-4065:SAG075_Main SAG075_Main RNA-Seq TRANSCRIPTOMIC Hybrid Selection 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. Illumina HiSeq 2500 Experimental Factor: main cell developmental stage ERX1220688 E-MTAB-4065:SAG077_Bud E-MTAB-4065:SAG077_Bud ERP013215 E-MTAB-4065 Expression profiling of budding cells in colorectal cancer suggests an EMT-like phenotype and molecular subtype switching ERS977615 SAMEA3670466 E-MTAB-4065:SAG077_Bud SAG077_Bud RNA-Seq TRANSCRIPTOMIC Hybrid Selection 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. Illumina HiSeq 2500 Experimental Factor: bud cell developmental stage ERX1220689 E-MTAB-4065:SAG078_Main E-MTAB-4065:SAG078_Main ERP013215 E-MTAB-4065 Expression profiling of budding cells in colorectal cancer suggests an EMT-like phenotype and molecular subtype switching ERS977616 SAMEA3670467 E-MTAB-4065:SAG078_Main SAG078_Main RNA-Seq TRANSCRIPTOMIC Hybrid Selection 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. Illumina HiSeq 2500 Experimental Factor: main cell developmental stage ERX1220690 E-MTAB-4065:SAG079_Bud E-MTAB-4065:SAG079_Bud ERP013215 E-MTAB-4065 Expression profiling of budding cells in colorectal cancer suggests an EMT-like phenotype and molecular subtype switching ERS977617 SAMEA3670468 E-MTAB-4065:SAG079_Bud SAG079_Bud RNA-Seq TRANSCRIPTOMIC Hybrid Selection 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. Illumina HiSeq 2500 Experimental Factor: bud cell developmental stage