characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2014-10-29T17:01:53Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T17:08:17Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA2337957
characteristics.characteristic: External Id
characteristics.text: Yale University
characteristics.characteristic: INSDC center name
characteristics.text: 2014-10-29T17:01:53Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T17:08:17Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS396153
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-2233:Rseq11
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: IMR90
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0001196
characteristics.characteristic: cell line
characteristics.text: fibroblast
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000057
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: IMR90 cells were cultured with MEM Earles media supplemented with 10% FBS 37C with 5% CO2 When cells are 80% confluent, Sendai Virus or media was added to the media and incubated for 6 hours at 37C. We have followed the protocol previously published in Core, L., Waterfall, J. & Lis, J. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845-1848 (2008). Briefly, nuclei from treated cells were isolated and incubated for 5 minutes with nucleotides and bromo-UTP analog. The nascent RNA from the labeling reaction was isolated and subjected to immunoaffinity purification using Br-dUTP antibody (Santa Cruz Biotech). After first round of purification of nascent RNA, the resulting RNA was ligated with 5' small RNA adaptor RNA (Illumina) and subjected to second Br-UTP purififcation. The resulting RNA is futher ligated using 3' adaptor RNA and subjected to third round of purification. The final purified RNA was reverse transcribed and PCR amplified and size selected (150-250bp) using polyacrylamide gel electrophoresis to generate the final sequencing library. A modified small RNA library contruction protocol based on the Illumina kit was modified and incorporated with the EXTRACTION PROTOCOL. Please see the EXTRACTION PROTOCOL for details.
characteristics.characteristic: description
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: female
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000383
characteristics.characteristic: sex
characteristics.text: 0 hour
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UO_0000032
characteristics.characteristic: time
characteristics.text: Rseq11
characteristics.characteristic: title