ERX1585175 E-MTAB-4893:T24KD_SCR-R2_s E-MTAB-4893:T24KD_SCR-R2_s ERP016337 Trim24 knock down in the 2i-state of the mouse ES cells ERS1233712 SAMEA4062602 T24KD_SCR-R2_s RNA-Seq TRANSCRIPTOMIC Oligo-dT 46c mouse ES cells were grown feeder-free on 0.2% gelatinized cell culture plates in 2i-media. The 2i-media contained DMEM/F12 media for SILAC (Pierce, 88215) supplemented 100 mg/ml of Lysine (Sigma, L8662), 100 mg/ml of Arginine (Sigma, A6969) and 100 mg/ml of Proline (Sigma, P5607), 100 microM MEM non-essential amino acids (Life technologies, 11140-050), 1xGlutamax (Life technologies, 35050-061), 1x penicillin and streptomycin (Life technologies, 15140-122), 100 microM of 2-mercaptoethanol (Sigma, M7522), 0.5mg/ml of BSA (Sigma, A3059), 200ng/ml of LIF (EMBL, protein expression core facility), 1microM of PD0325901(Reagents Direct, 39-C68), 3 microM of CHIR99021 (Reagents Direct, 27-H76). The cells were cultured using the 2i-media at least for 10 days, and passaged 4 times. The knock down (KD) was carried out by lentiviral transduction of : non-targeting shRNA, shTrim24 (TRCN0000088518), shTrp53 (TRCN0000310844), and the mixture of the last two shRNAs. For each knock down, 3 independent transductions was perfomed. For the details of virus production and infection please refer to PMID: 23260666. 48 hours after the viral treatment of the mouse ES cells, the cells were lysed, and RNA was extracted to be analyzed by qPCR and mRNA-seq RNA was extracted by Qiagen kit (RNeasy mini kit) mRNA-Seq libraries (from polyA+ cytoplasmic RNA) were created according to the standard Illumina TruSeq protocol. NextSeq 500 Experimental Factor: wild type genotype genotype ERX1585176 E-MTAB-4893:T24KD_Trim_p53_R3_s E-MTAB-4893:T24KD_Trim_p53_R3_s ERP016337 Trim24 knock down in the 2i-state of the mouse ES cells ERS1233713 SAMEA4062603 T24KD_Trim_p53_R3_s RNA-Seq TRANSCRIPTOMIC Oligo-dT 46c mouse ES cells were grown feeder-free on 0.2% gelatinized cell culture plates in 2i-media. The 2i-media contained DMEM/F12 media for SILAC (Pierce, 88215) supplemented 100 mg/ml of Lysine (Sigma, L8662), 100 mg/ml of Arginine (Sigma, A6969) and 100 mg/ml of Proline (Sigma, P5607), 100 microM MEM non-essential amino acids (Life technologies, 11140-050), 1xGlutamax (Life technologies, 35050-061), 1x penicillin and streptomycin (Life technologies, 15140-122), 100 microM of 2-mercaptoethanol (Sigma, M7522), 0.5mg/ml of BSA (Sigma, A3059), 200ng/ml of LIF (EMBL, protein expression core facility), 1microM of PD0325901(Reagents Direct, 39-C68), 3 microM of CHIR99021 (Reagents Direct, 27-H76). The cells were cultured using the 2i-media at least for 10 days, and passaged 4 times. The knock down (KD) was carried out by lentiviral transduction of : non-targeting shRNA, shTrim24 (TRCN0000088518), shTrp53 (TRCN0000310844), and the mixture of the last two shRNAs. For each knock down, 3 independent transductions was perfomed. For the details of virus production and infection please refer to PMID: 23260666. 48 hours after the viral treatment of the mouse ES cells, the cells were lysed, and RNA was extracted to be analyzed by qPCR and mRNA-seq RNA was extracted by Qiagen kit (RNeasy mini kit) mRNA-Seq libraries (from polyA+ cytoplasmic RNA) were created according to the standard Illumina TruSeq protocol. NextSeq 500 Experimental Factor: Trim24/Trp53 Knock Down genotype ERX1585177 E-MTAB-4893:T24KD_Trim-R1_s E-MTAB-4893:T24KD_Trim-R1_s ERP016337 Trim24 knock down in the 2i-state of the mouse ES cells ERS1233714 SAMEA4062604 T24KD_Trim-R1_s RNA-Seq TRANSCRIPTOMIC Oligo-dT 46c mouse ES cells were grown feeder-free on 0.2% gelatinized cell culture plates in 2i-media. The 2i-media contained DMEM/F12 media for SILAC (Pierce, 88215) supplemented 100 mg/ml of Lysine (Sigma, L8662), 100 mg/ml of Arginine (Sigma, A6969) and 100 mg/ml of Proline (Sigma, P5607), 100 microM MEM non-essential amino acids (Life technologies, 11140-050), 1xGlutamax (Life technologies, 35050-061), 1x penicillin and streptomycin (Life technologies, 15140-122), 100 microM of 2-mercaptoethanol (Sigma, M7522), 0.5mg/ml of BSA (Sigma, A3059), 200ng/ml of LIF (EMBL, protein expression core facility), 1microM of PD0325901(Reagents Direct, 39-C68), 3 microM of CHIR99021 (Reagents Direct, 27-H76). The cells were cultured using the 2i-media at least for 10 days, and passaged 4 times. The knock down (KD) was carried out by lentiviral transduction of : non-targeting shRNA, shTrim24 (TRCN0000088518), shTrp53 (TRCN0000310844), and the mixture of the last two shRNAs. For each knock down, 3 independent transductions was perfomed. For the details of virus production and infection please refer to PMID: 23260666. 48 hours after the viral treatment of the mouse ES cells, the cells were lysed, and RNA was extracted to be analyzed by qPCR and mRNA-seq RNA was extracted by Qiagen kit (RNeasy mini kit) mRNA-Seq libraries (from polyA+ cytoplasmic RNA) were created according to the standard Illumina TruSeq protocol. NextSeq 500 Experimental Factor: Trim24 Knock Down genotype ERX1585178 E-MTAB-4893:T24KD_SCR-R1_s E-MTAB-4893:T24KD_SCR-R1_s ERP016337 Trim24 knock down in the 2i-state of the mouse ES cells ERS1233715 SAMEA4062605 T24KD_SCR-R1_s RNA-Seq TRANSCRIPTOMIC Oligo-dT 46c mouse ES cells were grown feeder-free on 0.2% gelatinized cell culture plates in 2i-media. The 2i-media contained DMEM/F12 media for SILAC (Pierce, 88215) supplemented 100 mg/ml of Lysine (Sigma, L8662), 100 mg/ml of Arginine (Sigma, A6969) and 100 mg/ml of Proline (Sigma, P5607), 100 microM MEM non-essential amino acids (Life technologies, 11140-050), 1xGlutamax (Life technologies, 35050-061), 1x penicillin and streptomycin (Life technologies, 15140-122), 100 microM of 2-mercaptoethanol (Sigma, M7522), 0.5mg/ml of BSA (Sigma, A3059), 200ng/ml of LIF (EMBL, protein expression core facility), 1microM of PD0325901(Reagents Direct, 39-C68), 3 microM of CHIR99021 (Reagents Direct, 27-H76). The cells were cultured using the 2i-media at least for 10 days, and passaged 4 times. The knock down (KD) was carried out by lentiviral transduction of : non-targeting shRNA, shTrim24 (TRCN0000088518), shTrp53 (TRCN0000310844), and the mixture of the last two shRNAs. For each knock down, 3 independent transductions was perfomed. For the details of virus production and infection please refer to PMID: 23260666. 48 hours after the viral treatment of the mouse ES cells, the cells were lysed, and RNA was extracted to be analyzed by qPCR and mRNA-seq RNA was extracted by Qiagen kit (RNeasy mini kit) mRNA-Seq libraries (from polyA+ cytoplasmic RNA) were created according to the standard Illumina TruSeq protocol. NextSeq 500 Experimental Factor: wild type genotype genotype ERX1585179 E-MTAB-4893:T24KD_Trim-R2_s E-MTAB-4893:T24KD_Trim-R2_s ERP016337 Trim24 knock down in the 2i-state of the mouse ES cells ERS1233716 SAMEA4062606 T24KD_Trim-R2_s RNA-Seq TRANSCRIPTOMIC Oligo-dT 46c mouse ES cells were grown feeder-free on 0.2% gelatinized cell culture plates in 2i-media. The 2i-media contained DMEM/F12 media for SILAC (Pierce, 88215) supplemented 100 mg/ml of Lysine (Sigma, L8662), 100 mg/ml of Arginine (Sigma, A6969) and 100 mg/ml of Proline (Sigma, P5607), 100 microM MEM non-essential amino acids (Life technologies, 11140-050), 1xGlutamax (Life technologies, 35050-061), 1x penicillin and streptomycin (Life technologies, 15140-122), 100 microM of 2-mercaptoethanol (Sigma, M7522), 0.5mg/ml of BSA (Sigma, A3059), 200ng/ml of LIF (EMBL, protein expression core facility), 1microM of PD0325901(Reagents Direct, 39-C68), 3 microM of CHIR99021 (Reagents Direct, 27-H76). The cells were cultured using the 2i-media at least for 10 days, and passaged 4 times. The knock down (KD) was carried out by lentiviral transduction of : non-targeting shRNA, shTrim24 (TRCN0000088518), shTrp53 (TRCN0000310844), and the mixture of the last two shRNAs. For each knock down, 3 independent transductions was perfomed. For the details of virus production and infection please refer to PMID: 23260666. 48 hours after the viral treatment of the mouse ES cells, the cells were lysed, and RNA was extracted to be analyzed by qPCR and mRNA-seq RNA was extracted by Qiagen kit (RNeasy mini kit) mRNA-Seq libraries (from polyA+ cytoplasmic RNA) were created according to the standard Illumina TruSeq protocol. NextSeq 500 Experimental Factor: Trim24 Knock Down genotype ERX1585180 E-MTAB-4893:T24KD_Trim-R3_s E-MTAB-4893:T24KD_Trim-R3_s ERP016337 Trim24 knock down in the 2i-state of the mouse ES cells ERS1233717 SAMEA4062607 T24KD_Trim-R3_s RNA-Seq TRANSCRIPTOMIC Oligo-dT 46c mouse ES cells were grown feeder-free on 0.2% gelatinized cell culture plates in 2i-media. The 2i-media contained DMEM/F12 media for SILAC (Pierce, 88215) supplemented 100 mg/ml of Lysine (Sigma, L8662), 100 mg/ml of Arginine (Sigma, A6969) and 100 mg/ml of Proline (Sigma, P5607), 100 microM MEM non-essential amino acids (Life technologies, 11140-050), 1xGlutamax (Life technologies, 35050-061), 1x penicillin and streptomycin (Life technologies, 15140-122), 100 microM of 2-mercaptoethanol (Sigma, M7522), 0.5mg/ml of BSA (Sigma, A3059), 200ng/ml of LIF (EMBL, protein expression core facility), 1microM of PD0325901(Reagents Direct, 39-C68), 3 microM of CHIR99021 (Reagents Direct, 27-H76). The cells were cultured using the 2i-media at least for 10 days, and passaged 4 times. The knock down (KD) was carried out by lentiviral transduction of : non-targeting shRNA, shTrim24 (TRCN0000088518), shTrp53 (TRCN0000310844), and the mixture of the last two shRNAs. For each knock down, 3 independent transductions was perfomed. For the details of virus production and infection please refer to PMID: 23260666. 48 hours after the viral treatment of the mouse ES cells, the cells were lysed, and RNA was extracted to be analyzed by qPCR and mRNA-seq RNA was extracted by Qiagen kit (RNeasy mini kit) mRNA-Seq libraries (from polyA+ cytoplasmic RNA) were created according to the standard Illumina TruSeq protocol. NextSeq 500 Experimental Factor: Trim24 Knock Down genotype ERX1585181 E-MTAB-4893:T24KD_SCR-R3_s E-MTAB-4893:T24KD_SCR-R3_s ERP016337 Trim24 knock down in the 2i-state of the mouse ES cells ERS1233718 SAMEA4062608 T24KD_SCR-R3_s RNA-Seq TRANSCRIPTOMIC Oligo-dT 46c mouse ES cells were grown feeder-free on 0.2% gelatinized cell culture plates in 2i-media. The 2i-media contained DMEM/F12 media for SILAC (Pierce, 88215) supplemented 100 mg/ml of Lysine (Sigma, L8662), 100 mg/ml of Arginine (Sigma, A6969) and 100 mg/ml of Proline (Sigma, P5607), 100 microM MEM non-essential amino acids (Life technologies, 11140-050), 1xGlutamax (Life technologies, 35050-061), 1x penicillin and streptomycin (Life technologies, 15140-122), 100 microM of 2-mercaptoethanol (Sigma, M7522), 0.5mg/ml of BSA (Sigma, A3059), 200ng/ml of LIF (EMBL, protein expression core facility), 1microM of PD0325901(Reagents Direct, 39-C68), 3 microM of CHIR99021 (Reagents Direct, 27-H76). The cells were cultured using the 2i-media at least for 10 days, and passaged 4 times. The knock down (KD) was carried out by lentiviral transduction of : non-targeting shRNA, shTrim24 (TRCN0000088518), shTrp53 (TRCN0000310844), and the mixture of the last two shRNAs. For each knock down, 3 independent transductions was perfomed. For the details of virus production and infection please refer to PMID: 23260666. 48 hours after the viral treatment of the mouse ES cells, the cells were lysed, and RNA was extracted to be analyzed by qPCR and mRNA-seq RNA was extracted by Qiagen kit (RNeasy mini kit) mRNA-Seq libraries (from polyA+ cytoplasmic RNA) were created according to the standard Illumina TruSeq protocol. NextSeq 500 Experimental Factor: wild type genotype genotype ERX1585182 E-MTAB-4893:T24KD_Trim_p53_R1_s E-MTAB-4893:T24KD_Trim_p53_R1_s ERP016337 Trim24 knock down in the 2i-state of the mouse ES cells ERS1233719 SAMEA4062609 T24KD_Trim_p53_R1_s RNA-Seq TRANSCRIPTOMIC Oligo-dT 46c mouse ES cells were grown feeder-free on 0.2% gelatinized cell culture plates in 2i-media. The 2i-media contained DMEM/F12 media for SILAC (Pierce, 88215) supplemented 100 mg/ml of Lysine (Sigma, L8662), 100 mg/ml of Arginine (Sigma, A6969) and 100 mg/ml of Proline (Sigma, P5607), 100 microM MEM non-essential amino acids (Life technologies, 11140-050), 1xGlutamax (Life technologies, 35050-061), 1x penicillin and streptomycin (Life technologies, 15140-122), 100 microM of 2-mercaptoethanol (Sigma, M7522), 0.5mg/ml of BSA (Sigma, A3059), 200ng/ml of LIF (EMBL, protein expression core facility), 1microM of PD0325901(Reagents Direct, 39-C68), 3 microM of CHIR99021 (Reagents Direct, 27-H76). The cells were cultured using the 2i-media at least for 10 days, and passaged 4 times. The knock down (KD) was carried out by lentiviral transduction of : non-targeting shRNA, shTrim24 (TRCN0000088518), shTrp53 (TRCN0000310844), and the mixture of the last two shRNAs. For each knock down, 3 independent transductions was perfomed. For the details of virus production and infection please refer to PMID: 23260666. 48 hours after the viral treatment of the mouse ES cells, the cells were lysed, and RNA was extracted to be analyzed by qPCR and mRNA-seq RNA was extracted by Qiagen kit (RNeasy mini kit) mRNA-Seq libraries (from polyA+ cytoplasmic RNA) were created according to the standard Illumina TruSeq protocol. NextSeq 500 Experimental Factor: Trim24/Trp53 Knock Down genotype ERX1585183 E-MTAB-4893:T24KD_Trim_p53_R2_s E-MTAB-4893:T24KD_Trim_p53_R2_s ERP016337 Trim24 knock down in the 2i-state of the mouse ES cells ERS1233720 SAMEA4062610 T24KD_Trim_p53_R2_s RNA-Seq TRANSCRIPTOMIC Oligo-dT 46c mouse ES cells were grown feeder-free on 0.2% gelatinized cell culture plates in 2i-media. The 2i-media contained DMEM/F12 media for SILAC (Pierce, 88215) supplemented 100 mg/ml of Lysine (Sigma, L8662), 100 mg/ml of Arginine (Sigma, A6969) and 100 mg/ml of Proline (Sigma, P5607), 100 microM MEM non-essential amino acids (Life technologies, 11140-050), 1xGlutamax (Life technologies, 35050-061), 1x penicillin and streptomycin (Life technologies, 15140-122), 100 microM of 2-mercaptoethanol (Sigma, M7522), 0.5mg/ml of BSA (Sigma, A3059), 200ng/ml of LIF (EMBL, protein expression core facility), 1microM of PD0325901(Reagents Direct, 39-C68), 3 microM of CHIR99021 (Reagents Direct, 27-H76). The cells were cultured using the 2i-media at least for 10 days, and passaged 4 times. The knock down (KD) was carried out by lentiviral transduction of : non-targeting shRNA, shTrim24 (TRCN0000088518), shTrp53 (TRCN0000310844), and the mixture of the last two shRNAs. For each knock down, 3 independent transductions was perfomed. For the details of virus production and infection please refer to PMID: 23260666. 48 hours after the viral treatment of the mouse ES cells, the cells were lysed, and RNA was extracted to be analyzed by qPCR and mRNA-seq RNA was extracted by Qiagen kit (RNeasy mini kit) mRNA-Seq libraries (from polyA+ cytoplasmic RNA) were created according to the standard Illumina TruSeq protocol. NextSeq 500 Experimental Factor: Trim24/Trp53 Knock Down genotype ERX1585184 E-MTAB-4893:T24KD_p53-R1_s E-MTAB-4893:T24KD_p53-R1_s ERP016337 Trim24 knock down in the 2i-state of the mouse ES cells ERS1233721 SAMEA4062611 T24KD_p53-R1_s RNA-Seq TRANSCRIPTOMIC Oligo-dT 46c mouse ES cells were grown feeder-free on 0.2% gelatinized cell culture plates in 2i-media. The 2i-media contained DMEM/F12 media for SILAC (Pierce, 88215) supplemented 100 mg/ml of Lysine (Sigma, L8662), 100 mg/ml of Arginine (Sigma, A6969) and 100 mg/ml of Proline (Sigma, P5607), 100 microM MEM non-essential amino acids (Life technologies, 11140-050), 1xGlutamax (Life technologies, 35050-061), 1x penicillin and streptomycin (Life technologies, 15140-122), 100 microM of 2-mercaptoethanol (Sigma, M7522), 0.5mg/ml of BSA (Sigma, A3059), 200ng/ml of LIF (EMBL, protein expression core facility), 1microM of PD0325901(Reagents Direct, 39-C68), 3 microM of CHIR99021 (Reagents Direct, 27-H76). The cells were cultured using the 2i-media at least for 10 days, and passaged 4 times. The knock down (KD) was carried out by lentiviral transduction of : non-targeting shRNA, shTrim24 (TRCN0000088518), shTrp53 (TRCN0000310844), and the mixture of the last two shRNAs. For each knock down, 3 independent transductions was perfomed. For the details of virus production and infection please refer to PMID: 23260666. 48 hours after the viral treatment of the mouse ES cells, the cells were lysed, and RNA was extracted to be analyzed by qPCR and mRNA-seq RNA was extracted by Qiagen kit (RNeasy mini kit) mRNA-Seq libraries (from polyA+ cytoplasmic RNA) were created according to the standard Illumina TruSeq protocol. NextSeq 500 Experimental Factor: Trp53 Knock Down genotype ERX1585185 E-MTAB-4893:T24KD_p53-R2_s E-MTAB-4893:T24KD_p53-R2_s ERP016337 Trim24 knock down in the 2i-state of the mouse ES cells ERS1233722 SAMEA4062612 T24KD_p53-R2_s RNA-Seq TRANSCRIPTOMIC Oligo-dT 46c mouse ES cells were grown feeder-free on 0.2% gelatinized cell culture plates in 2i-media. The 2i-media contained DMEM/F12 media for SILAC (Pierce, 88215) supplemented 100 mg/ml of Lysine (Sigma, L8662), 100 mg/ml of Arginine (Sigma, A6969) and 100 mg/ml of Proline (Sigma, P5607), 100 microM MEM non-essential amino acids (Life technologies, 11140-050), 1xGlutamax (Life technologies, 35050-061), 1x penicillin and streptomycin (Life technologies, 15140-122), 100 microM of 2-mercaptoethanol (Sigma, M7522), 0.5mg/ml of BSA (Sigma, A3059), 200ng/ml of LIF (EMBL, protein expression core facility), 1microM of PD0325901(Reagents Direct, 39-C68), 3 microM of CHIR99021 (Reagents Direct, 27-H76). The cells were cultured using the 2i-media at least for 10 days, and passaged 4 times. The knock down (KD) was carried out by lentiviral transduction of : non-targeting shRNA, shTrim24 (TRCN0000088518), shTrp53 (TRCN0000310844), and the mixture of the last two shRNAs. For each knock down, 3 independent transductions was perfomed. For the details of virus production and infection please refer to PMID: 23260666. 48 hours after the viral treatment of the mouse ES cells, the cells were lysed, and RNA was extracted to be analyzed by qPCR and mRNA-seq RNA was extracted by Qiagen kit (RNeasy mini kit) mRNA-Seq libraries (from polyA+ cytoplasmic RNA) were created according to the standard Illumina TruSeq protocol. NextSeq 500 Experimental Factor: Trp53 Knock Down genotype