characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2017-06-15T17:01:31Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-05-16T18:32:20Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA104032928
characteristics.characteristic: External Id
characteristics.text: unspecified
characteristics.characteristic: INSDC center name
characteristics.text: 2017-06-15T17:01:31Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-05-16T18:32:20Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1696821
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-5714:AG11
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: HEK293T
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0001184
characteristics.characteristic: cell line
characteristics.text: epithelial cell
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000066
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: HEK293T cells were cultured in Dulbecco’s modified Eagle Medium (DMEM) (Life Technologies) containing 10% fetal bovine serum (Life Technologies), 2 mM glutamine (Life Technologies), 7mM MEM Non-Essential Amino Acids (Life Technologies), 1mM Sodium Pyruvate (Life Technologies), 10mM HEPES,100 units/ml penicillin streptomycin, and 100 μg/ml streptomycin (Life Technologies). Cells were co-transfected with constructs expressing 5’ and 3’ sgRNAs and pBABE-Puro in Opti-MEM® Reduced Serum Medium (Life Technologies) using the Lipofectamine® 3000 Reagent (Life Technologies). Cells were co-transfected in 48 well plates with either 0.75 μg of 5’sgRNA, 0.75 μg, 3’ sgRNA and 0.5 μg pBABE-Puro or 1.5 μg of empty PHI74 vector and 0.5 μg pBABE-Puro. 48 hours after transfection HEK293T cells were cultured for 14 days in the presence of Puromycin (0.75 μg/ml). 72 hours after transfection cells were split onto 10 cm dishes to ensure clonal growth. 10-14 days after splitting, clones were picked, amplified and tested for CRISPR-CaS11-mediated deletion by PCR. Homozygous clones were further amplified. Clones were harvested on different dates and pellets were frozen; however, all samples were processed simultaneously for DNA and RNA extraction (ATAC-seq and RNA-seq), library generation and sequencing. Total RNA was assessed for quality using an Agilent Tapestation Samples determined to have an RNA Integrity Number (RIN) of 7 or greater were used to generate RNA libraries using Illumina’s TruSeq Stranded Total RNA Sample Prep Kit
characteristics.characteristic: description
characteristics.text: chr8:579137-581436 deletion
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: kidney
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: AG11
characteristics.characteristic: title