characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2015-03-09T17:02:21Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T17:09:02Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA2341076
characteristics.characteristic: External Id
characteristics.text: EBML EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD
characteristics.characteristic: INSDC center name
characteristics.text: 2015-03-09T17:02:21Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T17:09:02Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS398747
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-2277:SH-SY5Y_shUnk_Unk_knockdown_replicate3
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: SH-SY5Y
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0002717
characteristics.characteristic: cell line
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: HeLa cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 micro-g/mL streptomycin at 37 degrees C and 5% CO2.' Lentiviral vectors (pLKO.1) harboring shRNAs targeting human Unkempt were obtained from Sigma (SHCLNG-NM_001080419). To knockdown Unkempt in mouse neurons, we modified the pSilencer1.0 GFP vector (Shen et al., Nature Genetics, 2010) by inserting between the ApaI and EcoRI sites the shRNAs targeting mouse Unkempt mRNA. The targeted sequences (shUnkW: CCCACTCTTCGTGCAGCACAA, shUnk: GGTATCACCTTCGTTACTA) were identified by the Broad Institute RNAi Consortium. SH-SY5Y cells were transfected at 40% confluence using Opti-MEM I Reduced Serum Medium and Lipofectamine 2000 (both Life Technologies) with a pool of siRNA targeting UNK (siGENOME SMART pool, M-022950-01) or a non-targeting siRNA pool (siGENOME Non-Targeting siRNA Pool 1; D-001206-13; both Thermo Scientific Dharmacon) at 25 nM. After 36 hours of transfection, cells were re-transfected with the above siRNA pools and incubated for an additional 24 hours.' Total RNA extracted from triplicates of each control and knockdown cells was DNase-treated and purified using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. RNA quality was assessed with the 2100 Bioanalyzer (Agilent Technologies).' Sequencing library preparation was carried out using TruSeq RNA Sample Preparation Kit v2 (Illumina).'
characteristics.characteristic: description
characteristics.text: Unk knockdown with shUnk
characteristics.characteristic: genotype
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: SH-SY5Y_shUnk_Unk_knockdown_replicate3
characteristics.characteristic: title