characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2021-10-02T00:28:07Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2021-10-02T00:28:07Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA10113423
characteristics.characteristic: External Id
characteristics.text: University of Toronto Ontario Institute of Cancer Research
characteristics.characteristic: INSDC center name
characteristics.text: 2021-10-02T00:28:07Z
characteristics.characteristic: INSDC first public
characteristics.text: 2021-10-02T00:28:07Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS7769977
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-10944:Sample 1
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: G797
characteristics.characteristic: cell line
characteristics.text: glial cell
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000125
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: G797 cells were maintained in serum-free NeuroCult™ NS-A Basal Medium (STEMCELL Technologies Canada Inc) supplemented with N2, B27, EGF (10 ng/ml), and FGF-2 (10 ng/ml). For overexpression, cells were transfected with pcDNA3.1-Neomycin-HOXA10-AS or the control vector pcDNA3.1-Neomycin using Lipofectamine 3000 Reagent (Thermo Fisher Scientific) as per manufacturer’s protocol. Two days post transfection, 500ug/ml G418 was added to select cells with stably expressing genes of interest for 2 weeks. Stable cells with overexpression of HOXA10-AS or the vector only were harvested for RNA extraction. Overexpression of HOXA10-AS was confirmed using RT-PCR. For knockdown, transfection of DsiRNAs was performed using the Lipofectamine RNAiMAX Reagent (Thermo Fisher Scientific) as per manufacturer’s protocol. Three days post transfection, cells were harvested for RNA extraction. RNAs were extracted from cells using Quick-RNA Microprep Kit (Zymo Research) as per manufacturer’s protocol. The quality of RNAs were assessed by Agilent Fragment Analyzer. The high quality RNAs were used to prepare the sequencing libraries. RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Prep Kit (20020594) as per manufacturer’s protocol. The barcoded cDNA libraries were then checked with Agilent Fragment Analyzer for fragment size and quantified with ddPCR (BioRad) using ddPCR™ Supermix for Probes (No dUTP) (BioRad cat#1863023) running in BioRad CFX96 Touch Real-Time PCR Detection System.
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: brain glioblastoma
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0000519
characteristics.characteristic: disease
characteristics.text: pcDNA3.1-HOXA10-AS
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: brain
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0000955
characteristics.characteristic: organism part
characteristics.text: HOXA10-AS overexpression
characteristics.characteristic: phenotype
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: Sample 1
characteristics.characteristic: title