ERS617398 SAMEA3146535 10090 Mus musculus Protocols: J1 (129S4/SvJae) and 129SvJae/Cast WT mESCs were grown under standard ESC culture conditions. Ring1A−/−;Ring1Bfl/fl;Rosa26::CreERT2 mESCs (Ring1A-KO) were cultured as described previously in Endoh et al. Dishes were coated with 0.1 % gelatine and irradiated mouse embryonic fibroblasts (MEFs). For harvesting, ESCs were trypsinized and pre-plated twice for 30 min to remove contaminating feeder cells. Mouse ESCs were washed in PBS and approximately 30-50 x 106 ES cells were lysed for 5 min in 0.5 ml cold buffer RLN (50 mM TrisHCl pH 7.5, 140 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 0.4% Igepal). Nuclei were pelleted by spinning at 300g for 10 min at 4°C. Nuclear RNA was isolated using TRIsure (Bioline), treated with DNaseI (Roche) and re-purified using an RNeasy Mini Kit (Qiagen). Strand-specific RNA-seq libraries were prepared as described previously by marking the second strand with dUTP but with some modifications8,9. 250 ng nuclear RNA was fragmented using a Covaris E220 instrument at standard RNA settings for 60 sec. Fragmented RNA was precipitated and first strand synthesis was carried out using SuperScript III (Invitrogen) with 4 µg of actinomycin D (Sigma). Nucleotides were removed with mini quick spin DNA columns (Roche) and second strand synthesis was performed using E.coli DNA ligase (NEB), DNA Polymerase I (NEB) and RNase H (Fermentas), replacing dTTP with dUTP (Fermentas). Following purification on QIAquick columns (Qiagen), TruSeq Illumina adapters were ligated with T4 DNA Ligase, (Enzymatics). Libraries were purified on QIAquick columns, treated with USER (NEB) to destroy the second strand and size selected using AMPure XP beads. Libraries were amplified with 9-11 PCR cycles. ENA-FIRST-PUBLIC 2015-08-01T17:04:24Z ENA-LAST-UPDATE 2018-03-08T22:13:32Z External Id SAMEA3146535 INSDC center name London Research Institute CRUK INSDC first public 2015-08-01T17:04:24Z INSDC last update 2018-03-08T22:13:32Z INSDC status public Submitter Id E-MTAB-3125:Ring1aKO_nuclear_RNA_seq_rep1 broker name ArrayExpress cell type embryonic stem cell common name house mouse genotype Ring1A−/−;Ring1Bfl/fl;R26::CreERT2 phenotype Ring1a knockout sample name E-MTAB-3125:Ring1aKO_nuclear_RNA_seq_rep1 scientific_name Mus musculus strain Ring1A−/−;Ring1Bfl/fl;R26::CreERT2 ERS617399 SAMEA3146536 10090 Mus musculus Protocols: J1 (129S4/SvJae) and 129SvJae/Cast WT mESCs were grown under standard ESC culture conditions. Ring1A−/−;Ring1Bfl/fl;Rosa26::CreERT2 mESCs (Ring1A-KO) were cultured as described previously in Endoh et al. Dishes were coated with 0.1 % gelatine and irradiated mouse embryonic fibroblasts (MEFs). For harvesting, ESCs were trypsinized and pre-plated twice for 30 min to remove contaminating feeder cells. Conditional deletion of Ring1B in Ring1A-KO cells was carried out by addition of 800 nM tamoxifen for 48 h as previously described in Endoh et al. Mouse ESCs were washed in PBS and approximately 30-50 x 106 ES cells were lysed for 5 min in 0.5 ml cold buffer RLN (50 mM TrisHCl pH 7.5, 140 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 0.4% Igepal). Nuclei were pelleted by spinning at 300g for 10 min at 4°C. Nuclear RNA was isolated using TRIsure (Bioline), treated with DNaseI (Roche) and re-purified using an RNeasy Mini Kit (Qiagen). Strand-specific RNA-seq libraries were prepared as described previously by marking the second strand with dUTP but with some modifications8,9. 250 ng nuclear RNA was fragmented using a Covaris E220 instrument at standard RNA settings for 60 sec. Fragmented RNA was precipitated and first strand synthesis was carried out using SuperScript III (Invitrogen) with 4 µg of actinomycin D (Sigma). Nucleotides were removed with mini quick spin DNA columns (Roche) and second strand synthesis was performed using E.coli DNA ligase (NEB), DNA Polymerase I (NEB) and RNase H (Fermentas), replacing dTTP with dUTP (Fermentas). Following purification on QIAquick columns (Qiagen), TruSeq Illumina adapters were ligated with T4 DNA Ligase, (Enzymatics). Libraries were purified on QIAquick columns, treated with USER (NEB) to destroy the second strand and size selected using AMPure XP beads. Libraries were amplified with 9-11 PCR cycles. ENA-FIRST-PUBLIC 2015-08-01T17:04:24Z ENA-LAST-UPDATE 2018-03-08T22:13:32Z External Id SAMEA3146536 INSDC center name London Research Institute CRUK INSDC first public 2015-08-01T17:04:24Z INSDC last update 2018-03-08T22:13:32Z INSDC status public Submitter Id E-MTAB-3125:Ring1a/b_dKO_nuclear_RNA_seq_rep1 broker name ArrayExpress cell type embryonic stem cell common name house mouse genotype Ring1A−/−;Ring1B-/- phenotype tamoxifen-mediated knockout of Ring1b on Ring1a-/- background sample name E-MTAB-3125:Ring1a/b_dKO_nuclear_RNA_seq_rep1 scientific_name Mus musculus strain Ring1A−/−;Ring1Bfl/fl;R26::CreERT2 ERS617400 SAMEA3146537 10090 Mus musculus Protocols: J1 (129S4/SvJae) and 129SvJae/Cast WT mESCs were grown under standard ESC culture conditions. Ring1A−/−;Ring1Bfl/fl;Rosa26::CreERT2 mESCs (Ring1A-KO) were cultured as described previously in Endoh et al. Dishes were coated with 0.1 % gelatine and irradiated mouse embryonic fibroblasts (MEFs). For harvesting, ESCs were trypsinized and pre-plated twice for 30 min to remove contaminating feeder cells. Mouse ESCs were washed in PBS and approximately 30-50 x 106 ES cells were lysed for 5 min in 0.5 ml cold buffer RLN (50 mM TrisHCl pH 7.5, 140 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 0.4% Igepal). Nuclei were pelleted by spinning at 300g for 10 min at 4°C. Nuclear RNA was isolated using TRIsure (Bioline), treated with DNaseI (Roche) and re-purified using an RNeasy Mini Kit (Qiagen). Strand-specific RNA-seq libraries were prepared as described previously by marking the second strand with dUTP but with some modifications8,9. 250 ng nuclear RNA was fragmented using a Covaris E220 instrument at standard RNA settings for 60 sec. Fragmented RNA was precipitated and first strand synthesis was carried out using SuperScript III (Invitrogen) with 4 µg of actinomycin D (Sigma). Nucleotides were removed with mini quick spin DNA columns (Roche) and second strand synthesis was performed using E.coli DNA ligase (NEB), DNA Polymerase I (NEB) and RNase H (Fermentas), replacing dTTP with dUTP (Fermentas). Following purification on QIAquick columns (Qiagen), TruSeq Illumina adapters were ligated with T4 DNA Ligase, (Enzymatics). Libraries were purified on QIAquick columns, treated with USER (NEB) to destroy the second strand and size selected using AMPure XP beads. Libraries were amplified with 9-11 PCR cycles. ENA-FIRST-PUBLIC 2015-08-01T17:04:24Z ENA-LAST-UPDATE 2018-03-08T22:13:32Z External Id SAMEA3146537 INSDC center name London Research Institute CRUK INSDC first public 2015-08-01T17:04:24Z INSDC last update 2018-03-08T22:13:32Z INSDC status public Submitter Id E-MTAB-3125:WT_nuclear_RNA_seq_rep2 broker name ArrayExpress cell type embryonic stem cell common name house mouse genotype wild type genotype phenotype wild type sample name E-MTAB-3125:WT_nuclear_RNA_seq_rep2 scientific_name Mus musculus strain J1 ERS617401 SAMEA3146538 10090 Mus musculus Protocols: J1 (129S4/SvJae) and 129SvJae/Cast WT mESCs were grown under standard ESC culture conditions. Ring1A−/−;Ring1Bfl/fl;Rosa26::CreERT2 mESCs (Ring1A-KO) were cultured as described previously in Endoh et al. Dishes were coated with 0.1 % gelatine and irradiated mouse embryonic fibroblasts (MEFs). For harvesting, ESCs were trypsinized and pre-plated twice for 30 min to remove contaminating feeder cells. Conditional deletion of Ring1B in Ring1A-KO cells was carried out by addition of 800 nM tamoxifen for 48 h as previously described in Endoh et al. Mouse ESCs were washed in PBS and approximately 30-50 x 106 ES cells were lysed for 5 min in 0.5 ml cold buffer RLN (50 mM TrisHCl pH 7.5, 140 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 0.4% Igepal). Nuclei were pelleted by spinning at 300g for 10 min at 4°C. Nuclear RNA was isolated using TRIsure (Bioline), treated with DNaseI (Roche) and re-purified using an RNeasy Mini Kit (Qiagen). Strand-specific RNA-seq libraries were prepared as described previously by marking the second strand with dUTP but with some modifications8,9. 250 ng nuclear RNA was fragmented using a Covaris E220 instrument at standard RNA settings for 60 sec. Fragmented RNA was precipitated and first strand synthesis was carried out using SuperScript III (Invitrogen) with 4 µg of actinomycin D (Sigma). Nucleotides were removed with mini quick spin DNA columns (Roche) and second strand synthesis was performed using E.coli DNA ligase (NEB), DNA Polymerase I (NEB) and RNase H (Fermentas), replacing dTTP with dUTP (Fermentas). Following purification on QIAquick columns (Qiagen), TruSeq Illumina adapters were ligated with T4 DNA Ligase, (Enzymatics). Libraries were purified on QIAquick columns, treated with USER (NEB) to destroy the second strand and size selected using AMPure XP beads. Libraries were amplified with 9-11 PCR cycles. ENA-FIRST-PUBLIC 2015-08-01T17:04:24Z ENA-LAST-UPDATE 2018-03-08T22:13:32Z External Id SAMEA3146538 INSDC center name London Research Institute CRUK INSDC first public 2015-08-01T17:04:24Z INSDC last update 2018-03-08T22:13:32Z INSDC status public Submitter Id E-MTAB-3125:Ring1a/b_dKO_nuclear_RNA_seq_rep2 broker name ArrayExpress cell type embryonic stem cell common name house mouse genotype Ring1A−/−;Ring1B-/- phenotype tamoxifen-mediated knockout of Ring1b on Ring1a-/- background sample name E-MTAB-3125:Ring1a/b_dKO_nuclear_RNA_seq_rep2 scientific_name Mus musculus strain Ring1A−/−;Ring1Bfl/fl;R26::CreERT2 ERS617402 SAMEA3146539 10090 Mus musculus Protocols: J1 (129S4/SvJae) and 129SvJae/Cast WT mESCs were grown under standard ESC culture conditions. Ring1A−/−;Ring1Bfl/fl;Rosa26::CreERT2 mESCs (Ring1A-KO) were cultured as described previously in Endoh et al. Dishes were coated with 0.1 % gelatine and irradiated mouse embryonic fibroblasts (MEFs). For harvesting, ESCs were trypsinized and pre-plated twice for 30 min to remove contaminating feeder cells. Mouse ESCs were washed in PBS and approximately 30-50 x 106 ES cells were lysed for 5 min in 0.5 ml cold buffer RLN (50 mM TrisHCl pH 7.5, 140 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 0.4% Igepal). Nuclei were pelleted by spinning at 300g for 10 min at 4°C. Nuclear RNA was isolated using TRIsure (Bioline), treated with DNaseI (Roche) and re-purified using an RNeasy Mini Kit (Qiagen). Strand-specific RNA-seq libraries were prepared as described previously by marking the second strand with dUTP but with some modifications8,9. 250 ng nuclear RNA was fragmented using a Covaris E220 instrument at standard RNA settings for 60 sec. Fragmented RNA was precipitated and first strand synthesis was carried out using SuperScript III (Invitrogen) with 4 µg of actinomycin D (Sigma). Nucleotides were removed with mini quick spin DNA columns (Roche) and second strand synthesis was performed using E.coli DNA ligase (NEB), DNA Polymerase I (NEB) and RNase H (Fermentas), replacing dTTP with dUTP (Fermentas). Following purification on QIAquick columns (Qiagen), TruSeq Illumina adapters were ligated with T4 DNA Ligase, (Enzymatics). Libraries were purified on QIAquick columns, treated with USER (NEB) to destroy the second strand and size selected using AMPure XP beads. Libraries were amplified with 9-11 PCR cycles. ENA-FIRST-PUBLIC 2015-08-01T17:04:24Z ENA-LAST-UPDATE 2018-03-08T22:13:32Z External Id SAMEA3146539 INSDC center name London Research Institute CRUK INSDC first public 2015-08-01T17:04:24Z INSDC last update 2018-03-08T22:13:32Z INSDC status public Submitter Id E-MTAB-3125:WT_nuclear_RNA_seq_rep1 broker name ArrayExpress cell type embryonic stem cell common name house mouse genotype wild type genotype phenotype wild type sample name E-MTAB-3125:WT_nuclear_RNA_seq_rep1 scientific_name Mus musculus strain J1 ERS617403 SAMEA3146540 10090 Mus musculus Protocols: J1 (129S4/SvJae) and 129SvJae/Cast WT mESCs were grown under standard ESC culture conditions. Ring1A−/−;Ring1Bfl/fl;Rosa26::CreERT2 mESCs (Ring1A-KO) were cultured as described previously in Endoh et al. Dishes were coated with 0.1 % gelatine and irradiated mouse embryonic fibroblasts (MEFs). For harvesting, ESCs were trypsinized and pre-plated twice for 30 min to remove contaminating feeder cells. Mouse ESCs were washed in PBS and approximately 30-50 x 106 ES cells were lysed for 5 min in 0.5 ml cold buffer RLN (50 mM TrisHCl pH 7.5, 140 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 0.4% Igepal). Nuclei were pelleted by spinning at 300g for 10 min at 4°C. Nuclear RNA was isolated using TRIsure (Bioline), treated with DNaseI (Roche) and re-purified using an RNeasy Mini Kit (Qiagen). Strand-specific RNA-seq libraries were prepared as described previously by marking the second strand with dUTP but with some modifications8,9. 250 ng nuclear RNA was fragmented using a Covaris E220 instrument at standard RNA settings for 60 sec. Fragmented RNA was precipitated and first strand synthesis was carried out using SuperScript III (Invitrogen) with 4 µg of actinomycin D (Sigma). Nucleotides were removed with mini quick spin DNA columns (Roche) and second strand synthesis was performed using E.coli DNA ligase (NEB), DNA Polymerase I (NEB) and RNase H (Fermentas), replacing dTTP with dUTP (Fermentas). Following purification on QIAquick columns (Qiagen), TruSeq Illumina adapters were ligated with T4 DNA Ligase, (Enzymatics). Libraries were purified on QIAquick columns, treated with USER (NEB) to destroy the second strand and size selected using AMPure XP beads. Libraries were amplified with 9-11 PCR cycles. ENA-FIRST-PUBLIC 2015-08-01T17:04:24Z ENA-LAST-UPDATE 2018-03-08T22:14:01Z External Id SAMEA3146540 INSDC center name London Research Institute CRUK INSDC first public 2015-08-01T17:04:24Z INSDC last update 2018-03-08T22:14:01Z INSDC status public Submitter Id E-MTAB-3125:Ring1aKO_nuclear_RNA_seq_rep2 broker name ArrayExpress cell type embryonic stem cell common name house mouse genotype Ring1A−/−;Ring1Bfl/fl;R26::CreERT2 phenotype Ring1a knockout sample name E-MTAB-3125:Ring1aKO_nuclear_RNA_seq_rep2 scientific_name Mus musculus strain Ring1A−/−;Ring1Bfl/fl;R26::CreERT2