E-MTAB-2830:Sample 18

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 18

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: clone13-4-high-IDE1-d2high Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: IDE1 endodermal diff

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 18


E-MTAB-2830:Sample 16

status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: European Molecular Biology Laboratory

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-2830:Sample 16

tag: Namespace:European Molecular Biology Laboratory

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: clone13-4-low-IDE1-d2 Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

characteristic: description

text: IDE1 endodermal diff

characteristic: growth condition

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Sample 16

characteristic: title

type: has member


E-MTAB-2830:Sample 6

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 6

text: ArrayExpress

text: house mouse

text: E14-diffmorphology-2 Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: lif+serum

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 6


E-MTAB-2830:Sample 29

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 29

text: ArrayExpress

text: house mouse

text: clonek12-IDE1-d6 Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: IDE1 endodermal diff

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 29


E-MTAB-2830:Sample 26

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 26

text: ArrayExpress

text: house mouse

text: clone13-4-high-IDE1-d3neg Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: IDE1 endodermal diff

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 26


E-MTAB-2830:Sample 3

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 3

text: ArrayExpress

text: house mouse

text: clone160-high Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: lif+serum

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 3


E-MTAB-2830:Sample 2

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 2

text: ArrayExpress

text: house mouse

text: clone99-low Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: lif+serum

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 2


E-MTAB-2830:Sample 24

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 24

text: ArrayExpress

text: house mouse

text: clone13-4-low-IDE1-d3low Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: IDE1 endodermal diff

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 24


E-MTAB-2830:Sample 21

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 21

text: ArrayExpress

text: house mouse

text: clone13-4-high-IDE1-d2low Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: IDE1 endodermal diff

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 21


E-MTAB-2830:Sample 19

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 19

text: ArrayExpress

text: house mouse

text: clone13-4-high-IDE1-d3high Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: IDE1 endodermal diff

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 19


E-MTAB-2830:Sample 27

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 27

text: ArrayExpress

text: house mouse

text: clone13-4-low-IDE1-d2neg Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: IDE1 endodermal diff

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 27


E-MTAB-2830:Sample 1

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 1

text: ArrayExpress

text: house mouse

text: clone99-high Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: lif+serum

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 1


E-MTAB-2830:Sample 10

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 10

text: ArrayExpress

text: house mouse

text: clonek12-2ibulk Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 10


E-MTAB-2830:Sample 4

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 4

text: ArrayExpress

text: house mouse

text: clone160-low Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: lif+serum

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 4


E-MTAB-2830:Sample 13

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 13

text: ArrayExpress

text: house mouse

text: clone13-4-2ilow Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 13


E-MTAB-2830:Sample 22

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 22

text: ArrayExpress

text: house mouse

text: clone13-4-high-IDE1-d3low Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: IDE1 endodermal diff

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 22


E-MTAB-2830:Sample 5

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 5

text: ArrayExpress

text: house mouse

text: E14-diffmorphology Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: lif+serum

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 5


E-MTAB-2830:Sample 12

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 12

text: ArrayExpress

text: house mouse

text: clone13-4-2ihigh Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 12


E-MTAB-2830:Sample 28

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 28

text: ArrayExpress

text: house mouse

text: clone13-4-low-IDE1-d3neg Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: IDE1 endodermal diff

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 28


E-MTAB-2830:Sample 23

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 23

text: ArrayExpress

text: house mouse

text: clone13-4-low-IDE1-d2low Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: IDE1 endodermal diff

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 23


E-MTAB-2830:Sample 7

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 7

text: ArrayExpress

text: house mouse

text: clone13-4-superhigh Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: lif+serum

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 7


E-MTAB-2830:Sample 9

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 9

text: ArrayExpress

text: house mouse

text: clone13-4-low Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: lif+serum

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 9


E-MTAB-2830:Sample 11

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 11

text: ArrayExpress

text: house mouse

text: clone13-4-2ibulk Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 11


E-MTAB-2830:Sample 17

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 17

text: ArrayExpress

text: house mouse

text: clone13-4-low-IDE1-d3 Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: IDE1 endodermal diff

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 17


E-MTAB-2830:Sample 8

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 8

text: ArrayExpress

text: house mouse

text: clone13-4-high Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: lif+serum

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 8


E-MTAB-2830:Sample 20

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 20

text: ArrayExpress

text: house mouse

text: clone13-4-low-IDE1-d3high Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: IDE1 endodermal diff

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 20


E-MTAB-2830:Sample 25

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 25

text: ArrayExpress

text: house mouse

text: clone13-4-high-IDE1-d2neg Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: IDE1 endodermal diff

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 25


E-MTAB-2830:Sample 14

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2830:Sample 14

text: ArrayExpress

text: house mouse

text: clone13-4-high-IDE1-d2 Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1 uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded mRNA libraries were prepared using TruSeq RNA Sample Preparation (Illumina) following the manufacturer's instructions.

text: IDE1 endodermal diff

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 14


E-MTAB-2831:Sample 15

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 15

text: ArrayExpress

text: house mouse

text: clone13-4-high-IDE1-d2high Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: IDE1 endodermal differentiation

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 15


E-MTAB-2831:Sample 18

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 18

text: ArrayExpress

text: house mouse

text: clone13-4-high-IDE1-d2neg Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: IDE1 endodermal differentiation

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 18


E-MTAB-2831:Sample 16

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 16

text: ArrayExpress

text: house mouse

text: clone13-4-high-IDE1-d3high Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: IDE1 endodermal differentiation

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 16


E-MTAB-2831:Sample 6

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 6

text: ArrayExpress

text: house mouse

text: clone13-4-low Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: lif+serum

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 6


E-MTAB-2831:Sample 3

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 3

text: ArrayExpress

text: house mouse

text: E14-diffmorphology Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: lif+serum

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 3


E-MTAB-2831:Sample 2

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 2

text: ArrayExpress

text: house mouse

text: clone99-low Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: lif+serum

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 2


E-MTAB-2831:Sample 21

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 21

text: ArrayExpress

text: house mouse

text: clonek12-IDE1-d6-2 Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: IDE1 endodermal differentiation

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 21


E-MTAB-2831:Sample 19

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 19

text: ArrayExpress

text: house mouse

text: clone13-4-low-IDE1-d2neg Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: IDE1 endodermal differentiation

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 19


E-MTAB-2831:Sample 1

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 1

text: ArrayExpress

text: house mouse

text: clone99-high Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: lif+serum

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 1


E-MTAB-2831:Sample 10

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 10

text: ArrayExpress

text: house mouse

text: clone13-4-2ilow Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 10


E-MTAB-2831:Sample 4

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 4

text: ArrayExpress

text: house mouse

text: clone13-4-superhigh Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: lif+serum

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 4


E-MTAB-2831:Sample 13

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 13

text: ArrayExpress

text: house mouse

text: clone13-4-low-IDE1-d2 Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: IDE1 endodermal differentiation

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 13


E-MTAB-2831:Sample 5

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 5

text: ArrayExpress

text: house mouse

text: clone13-4-high Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: lif+serum

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 5


E-MTAB-2831:Sample 12

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 12

text: ArrayExpress

text: house mouse

text: clone13-4-high-IDE1-d3 Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: IDE1 endodermal differentiation

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 12


E-MTAB-2831:Sample 7

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 7

text: ArrayExpress

text: house mouse

text: clonek12-2ibulk Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 7


E-MTAB-2831:Sample 8

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 8

text: ArrayExpress

text: house mouse

text: clone13-4-2ibulk Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 8


E-MTAB-2831:Sample 11

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 11

text: ArrayExpress

text: house mouse

text: clone13-4-high-IDE1-d2 Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: IDE1 endodermal differentiation

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 11


E-MTAB-2831:Sample 17

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 17

text: ArrayExpress

text: house mouse

text: clone13-4-high-IDE1-d2low Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: IDE1 endodermal differentiation

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 17


E-MTAB-2831:Sample 9

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 9

text: ArrayExpress

text: house mouse

text: clone13-4-2ihigh Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 9


E-MTAB-2831:Sample 20

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 20

text: ArrayExpress

text: house mouse

text: clonek12-IDE1-d6 Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: IDE1 endodermal differentiation

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 20


E-MTAB-2831:Sample 14

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-2831:Sample 14

text: ArrayExpress

text: house mouse

text: clone13-4-low-IDE1-d3 Protocols: Mouse ESCs were maintained without feeders in 'LIF+serum' medium (DMEM (high glucose, no glutamine, with sodium bicarbonate, Invitrogen) supplemented with 15% ES-qualified EmbryoMax Fetal Calf Serum (Millipore), 10 ng/ml murine LIF (EMBL Protein Expression and Purification Core Facility), 1x Non-Essential Amino Acids, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin and 100 ug/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37C with 5% CO2. Medium was changed daily and cells were passaged every other day with 0.05% Trypsin-EDTA (Invitrogen) at a passaging ratio of 1/6- 1/12. N2B27 medium was prepared from a 1:1 mixture of DMEM/F12 (without HEPES, with L-glutamine) and neurobasal medium with 0.5x B-27 (without vitamin A) and 0.5x N-2 supplements, 100 U/ml penicillin and 100 ug/ml streptomycin, 0.25 mM L-glutamine, 0.1 mM 2-mercaptoethanol (all Invitrogen), 10 ug/ml BSA fraction V and 10 ug/ml human recombinant insulin (both Sigma). '2i' medium was N2B27 medium supplemented with 3 uM CHIR99021 and 1uM PD0325901 (both Tocris Bioscience). mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 ug/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 uM IDE-1 (Tocris) following Borowiak et al. (Cell Stem Cell 2009). Barcoded miRNA libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) following the manufacturers instructions

text: IDE1 endodermal differentiation

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 14


text: public

tag: Namespace:Science for Life Laboratory, Royal Institute of Technology, Stockholm

text: ArrayExpress

text: human

text: Protocols: The tissue was homogenized mechanically using a 3 mm steel grinding ball (VWR). Total RNA was extracted from cell lines and tissue samples using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions. The extracted RNA samples were analyzed using either an Experion automated electrophoresis system (Bio-Rad Laboratories, Hercules, CA, USA) with the standard-sensitivity RNA chip or an Agilent 2100 Bioanalyzer system (Agilent Biotechnologies, Palo Alto, USA) with the RNA 6000 Nano Labchip Kit. Only samples of high-quality RNA (RNA Integrity Number 7.5) were used in the following mRNA sample preparation for sequencing. Libraries were contstructed using the Truseq v 2 kit, with poly-A-enrichmen

text: adult

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

text: rectum

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Science for Life Laboratory, Royal Institute of Technology, Stockholm

text: public

characteristic: Submitter Id

text: ArrayExpress

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: skeletal muscle

text: Homo sapiens

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: rectum

text: Homo sapiens

text: male


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: fallopian tube

text: Homo sapiens

text: female


text: public

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: adult

text: Homo sapiens

text: Homo sapiens

text: skeletal muscle

text: Homo sapiens

text: female


text: public

text: ArrayExpress

text: human

characteristic: description

text: adult

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: adipose tissue

text: Homo sapiens

text: female


text: public

text: ArrayExpress

text: human

text: adult

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

text: endometrium

text: Homo sapiens

text: female

characteristic: title


text: public

text: ArrayExpress

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: animal ovary

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: smooth muscle

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

text: public

characteristic: Submitter Id

text: ArrayExpress

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: tonsil

text: Homo sapiens

text: male


characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: colon

text: Homo sapiens

text: female


characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: tonsil

text: Homo sapiens

text: female


text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: human

text: adult

text: Homo sapiens

text: Homo sapiens

text: colon

text: Homo sapiens

text: male


text: Larval - Day 5 ZFS:0000037

characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped homozygous mutant embryo for nod2, allele sa18880,ZMP phenotype 71 clutch 1. A 8 base indexing sequence (ATCACGTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph71

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Larval - Day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single genotyped homozygous mutant embryo for nod2, allele sa18880,ZMP phenotype 71 clutch 1. A 8 base indexing sequence (CGATGTTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph71

text: Danio rerio

text: mixed


text: Larval - Day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped homozygous mutant embryo for nod2, allele sa18880,ZMP phenotype 71 clutch 1. A 8 base indexing sequence (TTAGGCAT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph71

text: Danio rerio

text: mixed


text: Larval - Day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

text: public

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped homozygous mutant embryo for nod2, allele sa18880,ZMP phenotype 71 clutch 1. A 8 base indexing sequence (TGACCACT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph71

text: Danio rerio

text: mixed


text: Larval - Day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped homozygous mutant embryo for nod2, allele sa18880,ZMP phenotype 71 clutch 1. A 8 base indexing sequence (ACAGTGGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph71

text: Danio rerio

text: mixed


text: Larval - Day 5 ZFS:0000037

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped homozygous mutant embryo for nod2, allele sa18880,ZMP phenotype 71 clutch 1. A 8 base indexing sequence (CAGATCTG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph71

text: Danio rerio

text: mixed


text: Larval - Day 5 ZFS:0000037

characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped homozygous mutant embryo for nod2, allele sa18880,ZMP phenotype 71 clutch 1. A 8 base indexing sequence (ACTTGATG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph71

text: Danio rerio

text: mixed


text: Larval - Day 5 ZFS:0000037

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped homozygous mutant embryo for nod2, allele sa18880,ZMP phenotype 71 clutch 1. A 8 base indexing sequence (GATCAGCG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph71

text: Danio rerio

text: mixed