characteristics.text: Pilot2
characteristics.characteristic: 1000 Genomes dataset
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2013-10-17T17:02:08Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T16:49:06Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA2223985
characteristics.characteristic: External Id
characteristics.text: University of Geneva Medical School, Department of Genetic Medicine and Development
characteristics.characteristic: INSDC center name
characteristics.text: 2013-10-17T17:02:08Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T16:49:06Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS360411
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-1885:NA12892
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: NA12892
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000895
characteristics.characteristic: cell line
characteristics.text: lymphoblastoid
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0000572
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: Lymphoblastoid cell lines were obtained from Coriell (http://ccr.coriell.org) and cultured in RPMI-1640 medium (Lonza) with 10% fetal calf serun (FCS). Frozen cells were thawed and transferred to T25 flasks containing 15 ml of medium. At a density of 0.3 x 10^6 cells/m cells were transferred to TubeSpin Bioreactor 50 tubes (TPP) in 5 ml of same medium containing 10% FCS and 0.1% Pluronic F-68 (Sigma-Aldrich). The cultures were agitated at 180 rpm with 5% CO2 and 85% humidity. When the cell density reached 2-3 x 10^6 cells/ml, the culture was diluted to 0.3 x 10^6 cells/ml and transferred to a 250-ml glass bottle. The culture was agitated at 110 rpm with 5% CO2 but no humidity. Eventually, the cells were scaled-up serially in 500-ml, 1-L, and 5-L glass bottles filled to a maximum of 40% of the nominal volume. Nuclei were isolated and nucleotides washed off at 4 degrees C, leaving RNA polymerases engaged in transcription bound to DNA. 5M nuclei per sample were then used for letting the polymerases run-on for ~100 nts using Br-UTP, alpha-P32-labeled CTP for tracking the nascent RNA through the experiment and sarkosyl for blocking new transcription initiation events. RNA was isolated and hydrolyzed. Subsequently, the nascent RNA was pulled down with agarose beads carrying antibodies for Br-UTP. 5' and 3' adapters were then ligated to nascent RNA, fulfilling another round of immuno-enrichment after each step. Finally, the nascent RNA library was converted to cDNA, PCR amplified and purified, yielding 2 libraries per sample. Given the way they were purified from the agarose gel, one library is of longer insert size (termed long) than the other (termed short). Sequencing libraries were prepared with TruSeq RNA Sample Prep Kit v2 high-throughput protocol (Illumina) according to manufacturer's instructions.
characteristics.characteristic: description
characteristics.text: NA12892
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000895
characteristics.characteristic: individual
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: HapMap CEU
characteristics.characteristic: population
characteristics.text: CEPH
characteristics.characteristic: population name
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: NA12892
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000895
characteristics.characteristic: title