characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2013-11-14T17:01:22Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T16:37:48Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA1929731
characteristics.characteristic: External Id
characteristics.text: Genecenter munich
characteristics.characteristic: INSDC center name
characteristics.text: 2013-11-14T17:01:22Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T16:37:48Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS329924
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-1766:Saccharomyces cerevisiae culture 2
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: baker's yeast
characteristics.characteristic: common name
characteristics.text: Protocols: Fresh yeast cells from agar plates were grown in YPD over night and diluted to a starting OD of 0.1 in the next morning. Cells were grown until OD 0.6. At OD 0.6 cell cultures were splitted in two and one half was treated with 1 ug/ml rapamycin for 60 min. After 60 min of rapamycin treatment all cultures were either treated with 4tU for 6 min (final concentration 5mM) or were cross-linked for 20 min using 1% formaldehyde. RNA was extracted as described (E-MTAB-760) and chromatin immunoprecipitations were performed as described in (E-TABM-1033) using an antibody against the Rpb3 subunit of Pol II (Neoclone, Catalog #: WP012). Once labeled RNA was purified it was subjected to Ribozero treatment following the manufactureres protocol with 1 ug of labeled RNA as input. rRNA depleted RNA was used to generate strand specific libraries using the NuGen Encore Complete RNA kit. ChIP-Seq libraries were created using the ChIP-Seq Kit from NEB (NEB, Cat# E6200) and Multiplex Oligos (NEB, Cat# E7335). PAR-CLIP was done with slight variations to another study (GEO: GSE31764) adapted for yeast and the protocol will be published in detail in another study.
characteristics.characteristic: description
characteristics.text: ade2-1 trp1-1 can1-100 leu2-3,-112 his3-11,-15 ura3 GAL psi+ tor1-1 fpr1::NAT, RPL13A-2xFKBP12::TRP1
characteristics.characteristic: genotype
characteristics.text: Saccharomyces cerevisiae
characteristics.characteristic: organism
characteristics.text: Saccharomyces cerevisiae
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_4932
characteristics.characteristic: organism
characteristics.text: Saccharomyces cerevisiae
characteristics.characteristic: scientific_name
characteristics.text: mating type alpha
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0001270
characteristics.characteristic: sex
characteristics.text: fresh specimen
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/OBI_0000971
characteristics.characteristic: specimen with known storage state
characteristics.text: W 303
characteristics.characteristic: strain
characteristics.text: Saccharomyces cerevisiae culture 2
characteristics.characteristic: title