characteristics.text: 2013-09-08T17:00:39Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T16:21:09Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA2060134
characteristics.characteristic: External Id
characteristics.text: EMBL-EBI
characteristics.characteristic: INSDC center name
characteristics.text: 2013-09-08T17:00:39Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T16:21:09Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS225446
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-1585:7sk_1c
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: Embryonic stem cell
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0002322
characteristics.characteristic: cell type
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: Oct4-GIP mouse embryonic stem (ES) cells (Ying et al. 2002) were cultured in either standard ES cell medium (GMEM with 10% fetal calf serum (Biosera), 0.1mM non-essential amino acids, 2mM L-Glutamine, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol and 106 units/L LIF (ESGRO, Millipore)), or in 2i/LIF medium (GMEM with 10% Knock-Out Serum Replacement (Life Technologies), 1% fetal calf serum (Biosera or Sigma), 0.1mM non-essential amino acids, 2mM L-Glutamine, sodium pyruvate, 0.1mM beta-mercaptoethanol, 1?M PD0325901 (AxonMedChem), 3?M CHIR99021 (AxonMedChem) and 106 units/L LIF (ESGRO, Millipore)). 1?g/ml puromycin was added to Oct4-GIP ES cell cultures during expansion. Total RNA was isolated using miRNeasy extraction kit (Qiagen) with in-column DNase treatment. Total RNA was depleted from ribosomal RNA with the Low Input Ribo-Zero rRNA removal system (Epicentre). rRNA-depleted samples were then fragmented with RNA fragmentation reagent (Ambion), purified using the RNeasy MinElute Kit (Qiagen) and treated with alkaline phosphatase (New England Biolabs) for 30 minutes at 37?C. 5' dephosphorylated RNA was treated with T4 PNK Kinase (New England Biolabs) for 60 minutes at 37?C. The resulting RNA (5' mono-phosphorylated and 3? OH) was purified with RNeasy MinElute (Qiagen) and ligated with RNA 3? and 5' TruSeq adapters (Illumina). Indexes 1-6 were used for PCR amplification.
characteristics.characteristic: description
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_10090
characteristics.characteristic: organism
characteristics.text: normal
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000461
characteristics.characteristic: phenotype
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: 129/Ola
characteristics.characteristic: strain
characteristics.text: 7sk_1c
characteristics.characteristic: title