ERX012726 E-MTAB-651:run 2 ERP000671 E-MTAB-651 RNAi of signal transduction components in HCT116 cells SRS024887 ERS033069 barcode_tag ERS033070 barcode_tag ERS033071 barcode_tag ERS033072 barcode_tag ERS033073 barcode_tag ERS033074 barcode_tag SS000025 OTHER TRANSCRIPTOMIC cDNA HCT116 cells were grown in McCoy's 5a medium (Invitrogen, Carlsbad, CA) supplemented with 10% FCS (PAA, Pasching , Austria) without antibiotics RNAi knockdown in HCT116 cells (ATCC) was performed by reverse transfection in 12 well format. Ambion silencer select RNAi reagents (Ambion) were used at 10nM final concentration using a 1:1000 final dilution ofDharmafect 1 (Dharmaon). Cells wer seeded at 100000 cells/well in a total volum of 1ml and incubated for 3 days. 2 wells were pooled for each treatment. Total RNA was extracted using the RNAeasy kit (Qiagen, Hilden, Germany). RNA integrity was verified on an Agient 2100 Bioanalyzer. mRNA was isolated with the Dynabeads mRNA DIRECT Kit (Invitrogen, Carlsbad,CA). For each sample, a library for SOLiD sequencing was prepared with the Whole transcriptome analysis kit (4409491 Rev. D, Invitrogen, Carlsbad,CA). Briefly, polyA RNA was fragmented using RNAseIII, purified, hybridized and ligated to RNA adapters. Ligation products were reverse transcribed, purified and ca. 200 nt cDNA fragments selected after electrophoresis on a 6% TBE-Urea gel. cDNA was PCR amplified with SOLiD sequencing primers and purified to produce a library suitable as a template for emulsion PCR. DNA concentrations were determined using qPCR and a pooled library was generated by combining equimolar amounts from all samples. 50 0 Application Read Forward 1 1 barcode_tag Technical Read BarCode AGGTTGCGAC GCGGTAAGCT GTGCGACACG AAGAGGAAAA GCGGTAAGGC GTGCGGCAGA AB SOLiD System 3.0 Experimental Factor: RNAI control Experimental Factor: RNAI APC Experimental Factor: RNAI CTNNB1 Experimental Factor: RNAI EVI Experimental Factor: RNAI BCL9 Experimental Factor: RNAI Axin1 ERX012725 E-MTAB-651:run 1 ERP000671 E-MTAB-651 RNAi of signal transduction components in HCT116 cells SRS024887 ERS033061 barcode_tag ERS033062 barcode_tag ERS033063 barcode_tag ERS033064 barcode_tag ERS033065 barcode_tag ERS033066 barcode_tag ERS033067 barcode_tag ERS033068 barcode_tag SS000017 OTHER TRANSCRIPTOMIC cDNA HCT116 cells were grown in McCoy's 5a medium (Invitrogen, Carlsbad, CA) supplemented with 10%%%%%%%% FCS (PAA, Pasching , Austria) without antibiotics RNAi knockdown in HCT116 cells (ATCC) was performed by reverse transfection in 12 well format. Ambion silencer select RNAi reagents (Ambion) were used at 10nM final concentration using a 1:1000 final dilution ofDharmafect 1 (Dharmaon). Cells wer seeded at 100000 cells/well in a total volum of 1ml and incubated for 3 days. 2 wells were pooled for each treatment. Total RNA was extracted using the RNAeasy kit (Qiagen, Hilden, Germany). RNA integrity was verified on an Agient 2100 Bioanalyzer. mRNA was isolated with the Dynabeads mRNA DIRECT Kit (Invitrogen, Carlsbad,CA). For each sample, a library for SOLiD sequencing was prepared with the Whole transcriptome analysis kit (4409491 Rev. D, Invitrogen, Carlsbad,CA). Briefly, polyA RNA was fragmented using RNAseIII, purified, hybridized and ligated to RNA adapters. Ligation products were reverse transcribed, purified and ca. 200 nt cDNA fragments selected after electrophoresis on a 6%%%%%%%% TBE-Urea gel. cDNA was PCR amplified with SOLiD sequencing primers and purified to produce a library suitable as a template for emulsion PCR. DNA concentrations were determined using qPCR and a pooled library was generated by combining equimolar amounts from all samples. 50 0 Application Read Forward 1 1 barcode_tag Technical Read BarCode GTGTAAGAGG AGGGAGTGGT ATAGGTTATA GGATGCGGTC GTGGTGTAAG GCGAGGGACA GGGTTATGCC GAGCGAGGAT AB SOLiD System 3.0 Experimental Factor: RNAI control Experimental Factor: RNAI APC Experimental Factor: RNAI CTNNB1 Experimental Factor: RNAI EVI Experimental Factor: RNAI BCL9 Experimental Factor: RNAI Axin1 Experimental Factor: RNAI TCF7L2 #1 Experimental Factor: RNAI TCF7L2 #2