ERX2090023 E-MTAB-5865:A1_p ERP024004 RNA-seq of coding RNA from USP14 knockout human haploid (HAP1) cells ERS1817636 SAMEA104158618 A1_p RNA-Seq TRANSCRIPTOMIC Oligo-dT HAP1 cells were derived from the near-haploid chronic myeloid leukaemia cell line KBM7 as described (Carette et al., 2011). HAP1 cells were cultured in IMDM supplemented with 10% FBS, penicillin-streptomycin and L-glutamine. Cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before harvesting total RNA Total RNA from 5 million cells was extracted using Qiagen RNeasy plus mini kit (74134). 1 μg of total RNA was subjected to library synthesis using the TruSeq RNA-Seq kit in technical replicate (e.g. two libraries were made from each RNA sample). 1 μg of total RNA was enriched for Poly-A mRNA using oligo dT-selection and reverse transcribed to cDNA. The cDNA was ligated with Illumina indexes. RNA libraries were prepared for sequencing using standard Illumina protocols. 70 0 F Application Read Forward 1 1 R Application Read Reverse 36 NextSeq 500 Experimental Factor: genotype wild type genotype ERX2090024 E-MTAB-5865:A2_p ERP024004 RNA-seq of coding RNA from USP14 knockout human haploid (HAP1) cells ERS1817636 SAMEA104158618 A2_p RNA-Seq TRANSCRIPTOMIC Oligo-dT HAP1 cells were derived from the near-haploid chronic myeloid leukaemia cell line KBM7 as described (Carette et al., 2011). HAP1 cells were cultured in IMDM supplemented with 10% FBS, penicillin-streptomycin and L-glutamine. Cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before harvesting total RNA Total RNA from 5 million cells was extracted using Qiagen RNeasy plus mini kit (74134). 1 μg of total RNA was subjected to library synthesis using the TruSeq RNA-Seq kit in technical replicate (e.g. two libraries were made from each RNA sample). 1 μg of total RNA was enriched for Poly-A mRNA using oligo dT-selection and reverse transcribed to cDNA. The cDNA was ligated with Illumina indexes. RNA libraries were prepared for sequencing using standard Illumina protocols. 70 0 F Application Read Forward 1 1 R Application Read Reverse 36 NextSeq 500 Experimental Factor: genotype wild type genotype ERX2090025 E-MTAB-5865:B1_p ERP024004 RNA-seq of coding RNA from USP14 knockout human haploid (HAP1) cells ERS1817637 SAMEA104158619 B1_p RNA-Seq TRANSCRIPTOMIC Oligo-dT HAP1 cells were derived from the near-haploid chronic myeloid leukaemia cell line KBM7 as described (Carette et al., 2011). HAP1 cells were cultured in IMDM supplemented with 10% FBS, penicillin-streptomycin and L-glutamine. Cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before harvesting total RNA Total RNA from 5 million cells was extracted using Qiagen RNeasy plus mini kit (74134). 1 μg of total RNA was subjected to library synthesis using the TruSeq RNA-Seq kit in technical replicate (e.g. two libraries were made from each RNA sample). 1 μg of total RNA was enriched for Poly-A mRNA using oligo dT-selection and reverse transcribed to cDNA. The cDNA was ligated with Illumina indexes. RNA libraries were prepared for sequencing using standard Illumina protocols. 70 0 F Application Read Forward 1 1 R Application Read Reverse 36 NextSeq 500 Experimental Factor: genotype wild type genotype ERX2090026 E-MTAB-5865:B2_p ERP024004 RNA-seq of coding RNA from USP14 knockout human haploid (HAP1) cells ERS1817637 SAMEA104158619 B2_p RNA-Seq TRANSCRIPTOMIC Oligo-dT HAP1 cells were derived from the near-haploid chronic myeloid leukaemia cell line KBM7 as described (Carette et al., 2011). HAP1 cells were cultured in IMDM supplemented with 10% FBS, penicillin-streptomycin and L-glutamine. Cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before harvesting total RNA Total RNA from 5 million cells was extracted using Qiagen RNeasy plus mini kit (74134). 1 μg of total RNA was subjected to library synthesis using the TruSeq RNA-Seq kit in technical replicate (e.g. two libraries were made from each RNA sample). 1 μg of total RNA was enriched for Poly-A mRNA using oligo dT-selection and reverse transcribed to cDNA. The cDNA was ligated with Illumina indexes. RNA libraries were prepared for sequencing using standard Illumina protocols. 70 0 F Application Read Forward 1 1 R Application Read Reverse 36 NextSeq 500 Experimental Factor: genotype wild type genotype ERX2090027 E-MTAB-5865:C1_p ERP024004 RNA-seq of coding RNA from USP14 knockout human haploid (HAP1) cells ERS1817638 SAMEA104158620 C1_p RNA-Seq TRANSCRIPTOMIC Oligo-dT HAP1 cells were derived from the near-haploid chronic myeloid leukaemia cell line KBM7 as described (Carette et al., 2011). HAP1 cells were cultured in IMDM supplemented with 10% FBS, penicillin-streptomycin and L-glutamine. Cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before harvesting total RNA Total RNA from 5 million cells was extracted using Qiagen RNeasy plus mini kit (74134). 1 μg of total RNA was subjected to library synthesis using the TruSeq RNA-Seq kit in technical replicate (e.g. two libraries were made from each RNA sample). 1 μg of total RNA was enriched for Poly-A mRNA using oligo dT-selection and reverse transcribed to cDNA. The cDNA was ligated with Illumina indexes. RNA libraries were prepared for sequencing using standard Illumina protocols. 70 0 F Application Read Forward 1 1 R Application Read Reverse 36 NextSeq 500 Experimental Factor: genotype USP14 knockout ERX2090028 E-MTAB-5865:C2_p ERP024004 RNA-seq of coding RNA from USP14 knockout human haploid (HAP1) cells ERS1817638 SAMEA104158620 C2_p RNA-Seq TRANSCRIPTOMIC Oligo-dT HAP1 cells were derived from the near-haploid chronic myeloid leukaemia cell line KBM7 as described (Carette et al., 2011). HAP1 cells were cultured in IMDM supplemented with 10% FBS, penicillin-streptomycin and L-glutamine. Cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before harvesting total RNA Total RNA from 5 million cells was extracted using Qiagen RNeasy plus mini kit (74134). 1 μg of total RNA was subjected to library synthesis using the TruSeq RNA-Seq kit in technical replicate (e.g. two libraries were made from each RNA sample). 1 μg of total RNA was enriched for Poly-A mRNA using oligo dT-selection and reverse transcribed to cDNA. The cDNA was ligated with Illumina indexes. RNA libraries were prepared for sequencing using standard Illumina protocols. 70 0 F Application Read Forward 1 1 R Application Read Reverse 36 NextSeq 500 Experimental Factor: genotype USP14 knockout ERX2090029 E-MTAB-5865:D1_p ERP024004 RNA-seq of coding RNA from USP14 knockout human haploid (HAP1) cells ERS1817639 SAMEA104158621 D1_p RNA-Seq TRANSCRIPTOMIC Oligo-dT HAP1 cells were derived from the near-haploid chronic myeloid leukaemia cell line KBM7 as described (Carette et al., 2011). HAP1 cells were cultured in IMDM supplemented with 10% FBS, penicillin-streptomycin and L-glutamine. Cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before harvesting total RNA Total RNA from 5 million cells was extracted using Qiagen RNeasy plus mini kit (74134). 1 μg of total RNA was subjected to library synthesis using the TruSeq RNA-Seq kit in technical replicate (e.g. two libraries were made from each RNA sample). 1 μg of total RNA was enriched for Poly-A mRNA using oligo dT-selection and reverse transcribed to cDNA. The cDNA was ligated with Illumina indexes. RNA libraries were prepared for sequencing using standard Illumina protocols. 70 0 F Application Read Forward 1 1 R Application Read Reverse 36 NextSeq 500 Experimental Factor: genotype USP14 knockout ERX2090030 E-MTAB-5865:D2_p ERP024004 RNA-seq of coding RNA from USP14 knockout human haploid (HAP1) cells ERS1817639 SAMEA104158621 D2_p RNA-Seq TRANSCRIPTOMIC Oligo-dT HAP1 cells were derived from the near-haploid chronic myeloid leukaemia cell line KBM7 as described (Carette et al., 2011). HAP1 cells were cultured in IMDM supplemented with 10% FBS, penicillin-streptomycin and L-glutamine. Cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before harvesting total RNA Total RNA from 5 million cells was extracted using Qiagen RNeasy plus mini kit (74134). 1 μg of total RNA was subjected to library synthesis using the TruSeq RNA-Seq kit in technical replicate (e.g. two libraries were made from each RNA sample). 1 μg of total RNA was enriched for Poly-A mRNA using oligo dT-selection and reverse transcribed to cDNA. The cDNA was ligated with Illumina indexes. RNA libraries were prepared for sequencing using standard Illumina protocols. 70 0 F Application Read Forward 1 1 R Application Read Reverse 36 NextSeq 500 Experimental Factor: genotype USP14 knockout