characteristic: ENA-CHECKLIST

text: School of Agriculture, Policy and Development University of Reading, UK

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: coconut palm

characteristic: common name

text: Protocols: Immature embryos (9ME) and mature embryos (12ME) were sampled from 25 years old (in 2010) Sri Lanka Tall coconut palms growing at Bandirippuwa Estate, Lunuwila Sri Lanka. Total RNA was extracted using an RNeasy Plant Mini Kit (Qiagen, UK) using manufacturers protocol. cDNA libraries were constructed using SMART approach as described by Zhu et al. 2001 using the the oligonucleotides SMART Sfi1A : 5prime- AAG CAG TGG TAT CAA CGC AGA GTG GCC ATT ACG GCCrGrGrG-3', CDS-Sfi1B : AAG CAG TGG TAT CAA CGC AGA GTG GCC GAG GCG GCCd(T)20-3', SMART PCR primer : 5'-AAG CAG TGG TAT CAA CGC AGA GT- 3'. The amplified cDNA PCR products were purified using QIAquick PCR Purification Kit (QIAGEN, CA) and a final yield of 3 microgram was prepared for each tissue type.

text: 9 months after pollination

characteristic: developmental stage

text: Immature

text: Sri Lanka Tall variety

text: Cocos nucifera

text: Cocos nucifera L.

text: Embryo

text: Cocos nucifera

text: frozen specimen


status: PUBLIC

tag: attribute

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:School of Agriculture, Policy and Development University of Reading, UK

text: ArrayExpress

characteristic: broker name

text: coconut palm

text: Protocols: Developing leaves (Leaf) were sampled in vitro germinated embryo culture plant (Weerakoon et al 2002). In vitro cultures were maintained at 28 degree centigrade under dark conditions in a culture room. Total RNA was extracted using an RNeasy Plant Mini Kit (Qiagen, UK) using manufacturers protocol. cDNA libraries were constructed using SMART approach as described by Zhu et al. 2001 using the the oligonucleotides SMART Sfi1A : 5prime- AAG CAG TGG TAT CAA CGC AGA GTG GCC ATT ACG GCCrGrGrG-3', CDS-Sfi1B : AAG CAG TGG TAT CAA CGC AGA GTG GCC GAG GCG GCCd(T)20-3', SMART PCR primer : 5'-AAG CAG TGG TAT CAA CGC AGA GT- 3'. The amplified cDNA PCR products were purified using QIAquick PCR Purification Kit (QIAGEN, CA) and a final yield of 3 microgram was prepared for each tissue type.

characteristic: description

text: 8 month old in vitro germinated coconut plantlet

text: Sri Lanka Tall variety

characteristic: genotype

text: Cocos nucifera

characteristic: organism

text: Cocos nucifera L.

text: leaf

characteristic: organism part

text: Cocos nucifera

text: frozen specimen

characteristic: specimen with known storage state

text: Leaf

characteristic: title

type: has member


characteristic: ENA-CHECKLIST

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: coconut palm

text: 12 months after pollination

text: Mature

characteristic: embryo classification

text: Sri Lanka Tall variety

text: Cocos nucifera

text: Cocos nucifera L.

text: Embryo

text: Cocos nucifera

text: frozen specimen


characteristic: ENA-FIRST-PUBLIC

text: European Molecular Biology Laboratory

text: public

tag: Namespace:European Molecular Biology Laboratory

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

characteristic: common name

text: Protocols: Grow single colony overnight in 5ml YPD at 30C unless the growth media is otherwise specified in sample annotations. Dilute in 50-100ml desired medium with starting OD600=0.1. Grow to OD600=1.0. Harvest cells for total RNA extraction. The exponentially growing cells were harvested at OD 0.6-0.9and broken with glass beads. An aliquot of lysate was taken as Input control, the remaining was subjected to immunoprecipitation (IP) with Dyna M280 sheep anti rabbit IgG for 2h at 4??C and analyzed as described previously (Gupta et al., 2014). Negative control IP was performed following the above procedure on a BY4741 strain without a Tap-tag on any protein. In summary 10 ??g of total RNA was fragmented, purified, retrotranscribed, end-repaired, ligated, amplified and finally size selected. Full protocol is describe in An efficient method for genome-wide polyadenylation site mapping and RNA quantification Wilkening et al., 2013

text: wild type genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: MAT_ leu2_20 ura3_met15_ lys2_ his3delta1 not1::NOT1-Tap-tag-URA3

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: European Molecular Biology Laboratory

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-3195:ZIP_polzm_Polzm_TE_Not1TT_wt_15

text: ArrayExpress

text: baker's yeast

text: Protocols: Grow single colony overnight in 5ml YPD at 30C unless the growth media is otherwise specified in sample annotations. Dilute in 50-100ml desired medium with starting OD600=0.1. Grow to OD600=1.0. Harvest cells for total RNA extraction. The polysome fraction was profiled henceforth was done as described in (Albanese et al., 2010). Briefly , 400 ml yeast in exponential growth phase was treated with 100 ??g/ml cycloheximide, harvested, washed with cold lysis buffer, resuspended in 1 ml of buffer A (20 mM Hepes, 50 mM KCl, 10 mM MgCl2, 1% Triton X-100, 1 mM DTT, and protease inhibitor cocktail), and frozen as drops in liquid nitrogen. The cells were ground and 1 ml of buffer A was added to the powder, and the lysates were clarified by centrifugation at 14,000 g for 10 min. 20 OD lysate was applied on a 12 ml 7???47% sucrose gradient in buffer A and centrifuged in a rotor (SW41; Beckman Coulter) for 150 min at 39,000 rpm at 4??C. Fractions were collected using a UA/6 detector (ISCO, Inc.). When indicated, polysomes were dissociated by treatment with 25 mM EDTA. The fractions were TCA precipitated, separated by SDS-PAGE, and subjected to immunoblot analysis. In summary 10 ??g of total RNA was fragmented, purified, retrotranscribed, end-repaired, ligated, amplified and finally size selected. Full protocol is describe in An efficient method for genome-wide polyadenylation site mapping and RNA quantification Wilkening et al., 2013

text: wild type genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: European Molecular Biology Laboratory

characteristic: INSDC last update

text: public

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: description

text: wild type genotype

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: European Molecular Biology Laboratory

text: public

text: E-MTAB-3195:ZIP_polzm_Polzm_TE_Not1TT_not5_16

text: ArrayExpress

text: baker's yeast

text: gene knock out

characteristic: genetic modification

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

characteristic: title


characteristic: ENA-CHECKLIST

text: European Molecular Biology Laboratory

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-3195:ZIP_polzm_Polzm_TE_Not1TT_not5_17

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


characteristic: ENA-FIRST-PUBLIC

text: European Molecular Biology Laboratory

text: public

text: E-MTAB-3195:ZIP_polzm_Polzm_TE_Not1TT_wt_19

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: baker's yeast

characteristic: common name

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: European Molecular Biology Laboratory

text: public

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: European Molecular Biology Laboratory

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-3195:ZIP_polzm_Polzm_TE_Not1TT_not5_20

text: ArrayExpress

text: baker's yeast

text: gene knock out

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


text: Plasmodium falciparum

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC last update

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: hypothalamic neurons

characteristic: ArrayExpress-OrganismPart

text: male

characteristic: ArrayExpress-Sex

text: House mouse

text: SC

text: public

text: house mouse

text: Mus musculus

text: library from single neurons

characteristic: sample description

text: Mus musculus


text: hypothalamic neurons

text: male

text: House mouse

text: SC

text: public

text: southeastern Asian house mouse

text: Mus musculus castaneus

characteristic: organism

text: library from single neurons

text: Mus musculus castaneus


text: hypothalamic neurons

text: male

text: House mouse

characteristic: ENA-CHECKLIST

text: SC

text: public

text: western European house mouse

text: Mus musculus domesticus

text: library from single neurons

text: Mus musculus domesticus


text: Shanghai Jiao Tong university

text: public

characteristic: INSDC status

tag: Namespace:Shanghai Jiao Tong university

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: gastrointestinal tract (lamina propria) macrophage

characteristic: cell type

text: human

text: Protocols: 10microgram of total RNA were purified using Oligotex mRNA Mini Kit (70022, QIAGEN) according to manufacturers instructions.

characteristic: description

text: gastric adenocarcinoma

characteristic: disease

text: EZH2 knockdown

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Shanghai Jiao Tong university

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: gastric adenocarcinoma

text: control

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: KI-BN

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: fruit fly

text: HT-SELEX generated data with following information on the name of the entry (Separated with underscores):Batch_BarcodeDesign_SelectionCycle

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: Abd-B


characteristic: ENA-CHECKLIST

text: KI-BN

text: public

characteristic: INSDC status

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: twi


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: sens


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: luna


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: btd


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: amos


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: cyc


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: rn


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: ovo


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: dpn


text: KI-BN

text: public

text: fruit fly

text: Drosophila melanogaster

text: Drosophila melanogaster

text: gl


text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: house mouse

text: Mus musculus

text: RNA for RNA-Seq Lib

characteristic: sample description

text: Mus musculus


text: public

tag: Namespace:Nanosafety & Nanomedicine Laboratory, Division of Molecular Toxicology, Institute of Environmental Medicine (IMM), Karolinska Institutet

text: ArrayExpress

characteristic: broker name

text: primary bronchial epithelial cell

characteristic: cell type

text: human

text: Protocols: The establishment of primary bronchial epithelial cells (PBECs) from human donors has been previously described (Strandberg, K.; Palmberg, L.; Larsson, K. Effect of formoterol and salmeterol on IL-6 and IL-8 release in airway epithelial cells. Respir. Med. 2007, 101, 1132-1139.) PBECs were exposure to PAMAMs Total RNA was extracted and purified from the cells and the samples were kept at -80C until further use. The mRNA Seq of polyadenylated transcripts from total RNA (samples are purified by poly-A enrichment before library creation using Illumina Tru-seq RNA) was used to profile nanoparticle treated and control samples at the Science for Life Laboratory, Stockholm, Sweden.

characteristic: description

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: lung

characteristic: organism part

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Nanosafety & Nanomedicine Laboratory, Division of Molecular Toxicology, Institute of Environmental Medicine (IMM), Karolinska Institutet

text: public

text: ArrayExpress

text: primary bronchial epithelial cell

text: human

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

characteristic: title


text: Mus musculus

characteristic: ArrayExpress-StrainOrLine

text: SC

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: ChipSeq library

text: Mus musculus

characteristic: strain


characteristic: ENA-CHECKLIST

text: UC SANTA CRUZ

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Bacterial Artificial Chromosome for chromosome Xq24

characteristic: Other Source

text: NatMethods_RP11_482A22.9RdsSpan.trim.fa.gz

tag: Namespace:UC SANTA CRUZ

text: Denisova hominin

text: BAC Reads

text: E. coli DH10B

characteristic: lab host

text: Homo sapiens ssp. Denisova

characteristic: organism

text: Homo sapiens ssp. Denisova

text: BAC Reads


characteristic: ENA-FIRST-PUBLIC

text: UC SANTA CRUZ

text: public

text: NatMethods_RP11_482A22.9RdsSpan.trim.maf.gz

text: Denisova hominin

text: BAC Multiple Alignment

characteristic: description

text: E. coli DH10B

text: Homo sapiens ssp. Denisova

text: Homo sapiens ssp. Denisova

text: BAC MAF


text: 11.5 weeks

characteristic: ArrayExpress-Age

text: Lin- bone marrow cells

characteristic: ArrayExpress-CellType

text: KO

characteristic: ArrayExpress-Genotype

text: wild type

characteristic: ArrayExpress-Phenotype

text: female

characteristic: ArrayExpress-Sex

text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: house mouse

text: Mus musculus

text: Lin- bone marrow cells

characteristic: sample description

text: Mus musculus


text: 11.5 weeks

text: Lin- bone marrow cells

text: WT

text: wild type

text: female

text: Mus Musculus

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: Lin- bone marrow cells

text: Mus musculus


text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

characteristic: organism

text: Input DNA; Library

text: Mus musculus


text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: ChIP-Seq Library

text: Mus musculus


text: male

text: Homo sapiens

text: SC

text: public

text: human

text: Homo sapiens

text: Total RNA

text: Homo sapiens


E-MTAB-3234:Sample 15

text: public

text: E-MTAB-3234:Sample 15

tag: Namespace:Cell Biology and Biophysics Unit. European Molecular BIology Laboratory

text: ArrayExpress

characteristic: broker name

text: embryonic stem cells

characteristic: cell type

text: house mouse

text: cloneK8_7-IDE1-d2-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 2 day

characteristic: differentiation day

text: IDE1 endodermal diff

characteristic: growth condition

text: mir142 +/-

characteristic: mir142 genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 15

characteristic: title


E-MTAB-3234:Sample 30

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Cell Biology and Biophysics Unit. European Molecular BIology Laboratory

text: public

text: E-MTAB-3234:Sample 30

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8_13-IDE1-d3-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 3 day

text: IDE1 endodermal diff

text: mir142 -/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 30


E-MTAB-3234:Sample 18

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-3234:Sample 18

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8_7-IDE1-d3-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 3 day

text: IDE1 endodermal diff

text: mir142 +/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 18


E-MTAB-3234:Sample 33

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-3234:Sample 33

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cells

text: house mouse

characteristic: common name

text: cloneK8_13-IDE1-d5-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 5 day

text: IDE1 endodermal diff

text: mir142 -/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 33


E-MTAB-3234:Sample 6

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3234:Sample 6

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8-IDE1-d3-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 3 day

text: IDE1 endodermal diff

text: mir142 +/+

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Sample 6


E-MTAB-3234:Sample 26

text: public

text: E-MTAB-3234:Sample 26

text: ArrayExpress

characteristic: broker name

text: embryonic stem cells

characteristic: cell type

text: house mouse

text: cloneK8_13-IDE1-d1-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 1 day

text: IDE1 endodermal diff

text: mir142 -/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 26


E-MTAB-3234:Sample 3

text: public

text: E-MTAB-3234:Sample 3

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8-IDE1-d2-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 2 day

characteristic: differentiation day

text: IDE1 endodermal diff

characteristic: growth condition

text: mir142 +/+

characteristic: mir142 genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 3


E-MTAB-3234:Sample 21

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-3234:Sample 21

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8_7-IDE1-d5-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 5 day

text: IDE1 endodermal diff

text: mir142 +/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 21

characteristic: title


E-MTAB-3234:Sample 24

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-3234:Sample 24

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8_7-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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 6 day

text: IDE1 endodermal diff

text: mir142 +/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 24


E-MTAB-3234:Sample 41

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: E-MTAB-3234:Sample 41

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: clone1225_IDE1-d3-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 3 day

text: IDE1 endodermal diff

text: constitutive miR-142 expression

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 41


E-MTAB-3234:Sample 36

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3234:Sample 36

text: ArrayExpress

text: embryonic stem cells

text: house mouse

characteristic: common name

text: cloneK8_13-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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 6 day

text: IDE1 endodermal diff

text: mir142 -/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 36


E-MTAB-3234:Sample 5

text: public

text: E-MTAB-3234:Sample 5

text: ArrayExpress

characteristic: broker name

text: embryonic stem cells

characteristic: cell type

text: house mouse

text: cloneK8-IDE1-d3-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 3 day

text: IDE1 endodermal diff

text: mir142 +/+

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Sample 5


E-MTAB-3234:Sample 22

text: public

text: E-MTAB-3234:Sample 22

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8_7-IDE1-d5-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 5 day

characteristic: differentiation day

text: IDE1 endodermal diff

characteristic: growth condition

text: mir142 +/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 22


E-MTAB-3234:Sample 39

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-3234:Sample 39

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: clone1225_IDE1-d2-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 2 day

text: IDE1 endodermal diff

text: constitutive miR-142 expression

characteristic: mir142 genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 39


E-MTAB-3234:Sample 46

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-3234:Sample 46

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: clone1225_IDE1-d5-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 5 day

text: IDE1 endodermal diff

text: constitutive miR-142 expression

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 46

characteristic: title


E-MTAB-3234:Sample 28

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-3234:Sample 28

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8_13-IDE1-d2-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 2 day

text: IDE1 endodermal diff

text: mir142 -/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 28


E-MTAB-3234:Sample 42

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3234:Sample 42

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: clone1225_IDE1-d3-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 3 day

text: IDE1 endodermal diff

text: constitutive miR-142 expression

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 42


E-MTAB-3234:Sample 23

text: Cell Biology and Biophysics Unit. European Molecular BIology Laboratory

text: public

text: E-MTAB-3234:Sample 23

text: ArrayExpress

characteristic: broker name

text: embryonic stem cells

characteristic: cell type

text: house mouse

characteristic: common name

text: cloneK8_7-IDE1-d6-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 6 day

text: IDE1 endodermal diff

text: mir142 +/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 23


E-MTAB-3234:Sample 43

text: public

text: E-MTAB-3234:Sample 43

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: clone1225_IDE1-d4-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 4 day

characteristic: differentiation day

text: IDE1 endodermal diff

text: constitutive miR-142 expression

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Sample 43


E-MTAB-3234:Sample 7

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-3234:Sample 7

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8-IDE1-d4-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 4 day

text: IDE1 endodermal diff

characteristic: growth condition

text: mir142 +/+

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 7


E-MTAB-3234:Sample 40

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-3234:Sample 40

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: clone1225_IDE1-d2-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 2 day

text: IDE1 endodermal diff

text: constitutive miR-142 expression

characteristic: mir142 genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 40


E-MTAB-3234:Sample 11

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

text: public

text: E-MTAB-3234:Sample 11

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8-IDE1-d6-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 6 day

text: IDE1 endodermal diff

text: mir142 +/+

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 11

characteristic: title


E-MTAB-3234:Sample 9

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-3234:Sample 9

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8-IDE1-d5-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 5 day

text: IDE1 endodermal diff

text: mir142 +/+

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 9


E-MTAB-3234:Sample 20

text: public

text: E-MTAB-3234:Sample 20

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: embryonic stem cells

characteristic: cell type

text: house mouse

text: cloneK8_7-IDE1-d4-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 4 day

text: IDE1 endodermal diff

text: mir142 +/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 20


E-MTAB-3234:Sample 31

text: public

text: E-MTAB-3234:Sample 31

text: ArrayExpress

text: embryonic stem cells

text: house mouse

characteristic: common name

text: cloneK8_13-IDE1-d4-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 4 day

characteristic: differentiation day

text: IDE1 endodermal diff

text: mir142 -/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 31


E-MTAB-3234:Sample 37

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-3234:Sample 37

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: clone1225_IDE1-d1-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 1 day

text: IDE1 endodermal diff

text: constitutive miR-142 expression

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Sample 37


E-MTAB-3234:Sample 38

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-3234:Sample 38

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: clone1225_IDE1-d1-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 1 day

text: IDE1 endodermal diff

characteristic: growth condition

text: constitutive miR-142 expression

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 38


E-MTAB-3234:Sample 16

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

text: public

text: E-MTAB-3234:Sample 16

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8_7-IDE1-d2-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 2 day

text: IDE1 endodermal diff

text: mir142 +/-

characteristic: mir142 genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 16


E-MTAB-3234:Sample 29

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3234:Sample 29

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8_13-IDE1-d3-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 3 day

text: IDE1 endodermal diff

text: mir142 -/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 29

characteristic: title


E-MTAB-3234:Sample 2

text: public

characteristic: SRA accession

text: E-MTAB-3234:Sample 2

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: embryonic stem cells

text: house mouse

text: cloneK8-IDE1-d1-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 1 day

text: IDE1 endodermal diff

text: mir142 +/+

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 2


E-MTAB-3234:Sample 19

text: public

text: E-MTAB-3234:Sample 19

text: ArrayExpress

text: embryonic stem cells

characteristic: cell type

text: house mouse

characteristic: common name

text: cloneK8_7-IDE1-d4-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 4 day

text: IDE1 endodermal diff

text: mir142 +/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 19


E-MTAB-3234:Sample 27

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-3234:Sample 27

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8_13-IDE1-d2-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 2 day

characteristic: differentiation day

text: IDE1 endodermal diff

text: mir142 -/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 27


E-MTAB-3234:Sample 1

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-3234:Sample 1

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8-IDE1-d1-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 1 day

text: IDE1 endodermal diff

text: mir142 mir142 +/+

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Sample 1


E-MTAB-3234:Sample 44

characteristic: ENA-FIRST-PUBLIC

text: Cell Biology and Biophysics Unit. European Molecular BIology Laboratory

characteristic: INSDC first public

text: public

text: E-MTAB-3234:Sample 44

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: clone1225_IDE1-d4-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 4 day

text: IDE1 endodermal diff

characteristic: growth condition

text: constitutive miR-142 expression

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 44


E-MTAB-3234:Sample 10

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3234:Sample 10

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8-IDE1-d5-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 5 day

text: IDE1 endodermal diff

text: mir142 +/+

characteristic: mir142 genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 10


E-MTAB-3234:Sample 4

text: public

characteristic: SRA accession

text: E-MTAB-3234:Sample 4

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8-IDE1-d2-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 2 day

text: IDE1 endodermal diff

text: mir142 +/+

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 4

characteristic: title


E-MTAB-3234:Sample 13

text: public

text: E-MTAB-3234:Sample 13

text: ArrayExpress

characteristic: broker name

text: embryonic stem cells

characteristic: cell type

text: house mouse

characteristic: common name

text: cloneK8_7-IDE1-d1-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 1 day

text: IDE1 endodermal diff

text: mir142 +/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 13


E-MTAB-3234:Sample 47

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-3234:Sample 47

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: clone1225_IDE1-d6-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 6 day

text: IDE1 endodermal diff

text: constitutive miR-142 expression

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 47


E-MTAB-3234:Sample 12

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-3234:Sample 12

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8-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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 6 day

characteristic: differentiation day

text: IDE1 endodermal diff

text: mir142 +/+

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 12


E-MTAB-3234:Sample 35

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

text: public

text: E-MTAB-3234:Sample 35

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8_13-IDE1-d6-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 6 day

text: IDE1 endodermal diff

text: mir142 -/-

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Sample 35


E-MTAB-3234:Sample 8

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3234:Sample 8

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8-IDE1-d4-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 4 day

text: IDE1 endodermal diff

characteristic: growth condition

text: mir142 +/+

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 8


E-MTAB-3234:Sample 34

text: public

characteristic: SRA accession

text: E-MTAB-3234:Sample 34

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8_13-IDE1-d5-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 5 day

text: IDE1 endodermal diff

text: mir142 -/-

characteristic: mir142 genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 34


E-MTAB-3234:Sample 17

text: public

text: E-MTAB-3234:Sample 17

text: ArrayExpress

characteristic: broker name

text: embryonic stem cells

characteristic: cell type

text: house mouse

text: cloneK8_7-IDE1-d3-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 3 day

text: IDE1 endodermal diff

text: mir142 +/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 17

characteristic: title


E-MTAB-3234:Sample 14

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-3234:Sample 14

text: ArrayExpress

text: embryonic stem cells

text: house mouse

characteristic: common name

text: cloneK8_7-IDE1-d1-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 1 day

text: IDE1 endodermal diff

text: mir142 +/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 14


E-MTAB-3234:Sample 25

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-3234:Sample 25

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8_13-IDE1-d1-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 1 day

text: IDE1 endodermal diff

text: mir142 -/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 25


E-MTAB-3234:Sample 45

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

text: public

text: E-MTAB-3234:Sample 45

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: clone1225_IDE1-d5-1 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 5 day

characteristic: differentiation day

text: IDE1 endodermal diff

text: constitutive miR-142 expression

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 45


E-MTAB-3234:Sample 32

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3234:Sample 32

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: cloneK8_13-IDE1-d4-2 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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 4 day

text: IDE1 endodermal diff

text: mir142 -/-

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Sample 32


E-MTAB-3234:Sample 48

text: public

characteristic: SRA accession

text: E-MTAB-3234:Sample 48

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cells

text: house mouse

text: clone1225_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 microgram/ml strep- tomycin, 0.1 mM 2-mercaptoethanol (all Invitrogen) on culture dishes (Nunc) coated with 0.1% gelatin (Sigma) solution and cultured at 37 degree centigrade 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. mESCs were differentiated to endoderm precursors in Advanced RPMI, 100 U/ml penicillin and 100 microgram/ml streptomycin (both Invitrogen), 0.2% FCS (EmbryoMax, Millipore), 1 microgramM 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: 6 day

text: IDE1 endodermal diff

characteristic: growth condition

text: constitutive miR-142 expression

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 48


text: public

text: E-MTAB-2972:Deckers_lab_Sep2014_STAT2_untreated

tag: Namespace:Institute of Animal Breeding & Genetics, University of Veterinary Medicine Vienna

text: ArrayExpress

characteristic: broker name

text: bone marrow macrophage

characteristic: cell type

text: house mouse

text: Protocols: Bone marrow-derived macrophages (BMDM) were obtained by culture of mouse bone marrow in DMEM +10%FCS +10% L-cell-derived conditioned medium containing colony-stimulating factor 1. After 10 days the cells were used for experiment. 2.5x107 cells were seeded on a 15cm dish and treated as follows. Cells used for ChIPseq experiments with antibodies against STAT1 were treated with 250U/ml IFNb for 2 hours. Cells subjected to ChIP with antibodies against NFkB p65 or RNA polymerase II were treated with IFNb (250U/ml) and hkL (equivalent to MOI 50) for 4 hours. After treatment formaldehyde was added to the cells to a final concentration of 1% and dishes were incubated for 10 minutes at 37°C. The reaction was quenched by adding 2.5 M glycine to a final concentration of 125 mM for 10 minutes. The fixed cells were washed with PBS and scraped. After centrifugation for 10 minutes at 600g cells were washed with wash I (0.25%Triton X-100; 0.01M EDTA; 0.5mM EGTA; 0.01M Hepes) for 10 minutes at 4°C, followed by another centrifugation step. The pellet was resuspended in wash II (0.2M NaCl; 1mM EDTA; 0.5mM EGTA; 0.01M Hepes) and kept for 10 minutes at 4°C. Cells were lysed over night with lysis buffer (1% SDS; 0.05M Tris pH 8; 0.01M EDTA) at 4°C. The cells were then sonicated 27 x 30 seconds using a Bioruptor sonicator. This resulted in chromatin fragments with an average length of 300 bp. Samples were centrifuged twice at 16.000g for 15 min and the supernatant was used for the subsequent steps. 5 ug antibody was added to the chromatin and rotated overnight at 4°C. Protein G Dynabeads (Invitrogen) were blocked over night in 0.1% BSA and on the next day added to the chromatin/antibody mixture and incuabted for 3 hours at 4°C. Beads were then washed five times for 10 minutes in RIPA buffer (0.15M NaCl; 0.05M Tris pH 8; 0.1% SDS; 0.5% NaDoc; 1% NP40), once in high salt buffer (0.5M NaCl; 0.05M Tris pH 8; 0.1% SDS; 1% NP40), once in LiCl buffer (0.25M LiCl; 0.05M Tris pH 8; 0.5% NaDoc; 1% NP40), and two times in TE buffer. Beads were then shaken in elution buffer at room temperature for 40 minutes and 20ul 4M NaCl was added to the eluted sample. Samples were incubated at 65°C overnight to reverse the cross-links. Samples were then treated with proteinase K (2ul ptroteinase K, 8ul EDTA 0.5M pH 7.5 and16ul IM TRIS pH 6.5) for 60 min at 55°C. 500ul Phenol/Chloroform/Isoamyl alcohol (25/24/1) was added to all samples and they were then centrifuged for 5 minutes at 16000g. The upper phase was used for DNA precipitation. 5-10 ng of DNA precipitate was used for the generation of sequencing libraries using the KAPA library preparation kit for Illumina systems. Libraries were quantified with a Bioanalyzer dsDNA 1000 assay kit (Agilent) and a QPCR NGS library quantification kit (KAPA).

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Institute of Animal Breeding & Genetics, University of Veterinary Medicine Vienna

text: public

text: E-MTAB-2972:Deckers_lab_Sep2014_STAT2_IFNb

text: ArrayExpress

text: bone marrow macrophage

text: house mouse

characteristic: common name

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: female

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: University of Southampton

characteristic: INSDC center name

text: public

tag: Namespace:University of Southampton

text: ArrayExpress

characteristic: cell line

text: foetal foreskin fibroblast

text: human

text: Five hundred thousand HFFF2 cultured for seven days Protocols: Human Foetal Foreskin Fibroblasts 2 (HFFF2) are cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% Foetal Bovine Serum and 292 ug/ml L-Glutamine. They have been treated with 2ng/ml TGF-beta-1 to induce myofibroblast differentiation or with 10Gy gamma irradiation to induce senescence. We isolated RNA 7 days upon this treatment changing medium 3 days bbefore the RNA extraction using RNAeasy minikit from Qiagen The kit we used is \Truseq Stranded mRNA\ sample prep kit from Illumina. Basic principle for stranded RNA library preparation is that dUTP is incorporated in the second strand synthesis of the cDNA. After adapter ligation, the dUTP strand is degraded by Uricil-DNA-Glycosylase (UDG) and the remaining strand is then amplified to make the Illumina library. However, Illumina uses polymerase I which is intolerant to dUTP, thus it just does not amplify the strand with dUTP incorporated. More details can be found in the Illumina’s Guide on page 2 in the link down here: http://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedmrna/truseq-stranded-mrna-sample-prep-guide-15031047-e.pdf

characteristic: description

text: DMEM supplemented 10% FBS and 10% CO2

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: University of Southampton

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: foetal foreskin fibroblast

text: human

text: Five hundred thousand HFFF2 irradiated at a dose of 10Grey and cultured for seven days Protocols: Human Foetal Foreskin Fibroblasts 2 (HFFF2) are cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% Foetal Bovine Serum and 292 ug/ml L-Glutamine. They have been treated with 2ng/ml TGF-beta-1 to induce myofibroblast differentiation or with 10Gy gamma irradiation to induce senescence. We isolated RNA 7 days upon this treatment changing medium 3 days bbefore the RNA extraction using RNAeasy minikit from Qiagen The kit we used is \Truseq Stranded mRNA\ sample prep kit from Illumina. Basic principle for stranded RNA library preparation is that dUTP is incorporated in the second strand synthesis of the cDNA. After adapter ligation, the dUTP strand is degraded by Uricil-DNA-Glycosylase (UDG) and the remaining strand is then amplified to make the Illumina library. However, Illumina uses polymerase I which is intolerant to dUTP, thus it just does not amplify the strand with dUTP incorporated. More details can be found in the Illumina’s Guide on page 2 in the link down here: http://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedmrna/truseq-stranded-mrna-sample-prep-guide-15031047-e.pdf

text: DMEM supplemented 10% FBS and 10% CO2

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens


text: University of Southampton

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: foetal foreskin fibroblast

text: human

text: Five hundred thousand HFFF2 treated with TGF-beta 1 at a concentration of 2ng/ml and cultured for seven days Protocols: Human Foetal Foreskin Fibroblasts 2 (HFFF2) are cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% Foetal Bovine Serum and 292 ug/ml L-Glutamine. They have been treated with 2ng/ml TGF-beta-1 to induce myofibroblast differentiation or with 10Gy gamma irradiation to induce senescence. We isolated RNA 7 days upon this treatment changing medium 3 days bbefore the RNA extraction using RNAeasy minikit from Qiagen The kit we used is \Truseq Stranded mRNA\ sample prep kit from Illumina. Basic principle for stranded RNA library preparation is that dUTP is incorporated in the second strand synthesis of the cDNA. After adapter ligation, the dUTP strand is degraded by Uricil-DNA-Glycosylase (UDG) and the remaining strand is then amplified to make the Illumina library. However, Illumina uses polymerase I which is intolerant to dUTP, thus it just does not amplify the strand with dUTP incorporated. More details can be found in the Illumina’s Guide on page 2 in the link down here: http://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_truseq/truseqstrandedmrna/truseq-stranded-mrna-sample-prep-guide-15031047-e.pdf

text: DMEM supplemented 10% FBS and 10% CO2

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

text: public

text: house mouse

text: Mus musculus

characteristic: sample description

text: Mus musculus


text: iPS Cells

characteristic: ArrayExpress-CellType

text: Epiblast

characteristic: ArrayExpress-OrganismPart

text: iPS

characteristic: ArrayExpress-Phenotype

text: Mus Musculus

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

text: gRNA PCR

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Genomnia srl

characteristic: INSDC center name

text: public

tag: Namespace:Genomnia srl

text: ArrayExpress

text: human

text: Protocols: RMS tumour samples were obtained at diagnosis before any treatment from children admitted to the Department of Paediatrics and Infantile Neuropsychiatry at Sapienzu University of Rome, and to the Department of Oncology at Alder Hey Childrens NHS Trust, Liverpool. Histopathological diagnosis was confirmed using immunohistochemistry. Total RNA was extracted using Trizol reagent, according to the manufacturers instructions. Samples were enriched for small RNAs up to 200 bp by size selection using Pure Link miRNA Isolation Kit (LifeTech). Enriched RNA samples were processed using the Small RNA Expression Kit according to the manufacturers protocol (Small RNA expression kit, rev. C, Applied Biosystems). cDNA libraries were barcoded using the Solid RNA barcoding kit and amplified onto beads using emulsion PCR. Templated beads were deposited on slides and analysed using the Applied Biosystems SOLiD 4 Sequencer

characteristic: description

text: no disease

characteristic: disease

text: no disease

characteristic: disease staging

text: Homo sapiens

text: Homo sapiens

text: skeletal muscle

characteristic: organism part

text: Homo sapiens

text: NSM

characteristic: title