characteristics.text: SAMN20063635
characteristics.characteristic: External Id
characteristics.text: National Cancer Institute
characteristics.characteristic: INSDC center name
characteristics.text: 2022-05-10T00:00:00Z
characteristics.characteristic: INSDC first public
characteristics.text: 2022-05-10T16:32:02.220Z
characteristics.characteristic: INSDC last update
characteristics.text: SRS9402523
characteristics.characteristic: INSDC secondary accession
characteristics.text: live
characteristics.characteristic: INSDC status
characteristics.text: Human
characteristics.characteristic: NCBI submission model
characteristics.text: Human.1.0
characteristics.characteristic: NCBI submission package
characteristics.text: SRS9402523
characteristics.characteristic: SRA accession
characteristics.text: 58
characteristics.characteristic: age
characteristics.text: ATCC
characteristics.characteristic: biomaterial_provider
characteristics.text: HT-1376
characteristics.characteristic: cell_line
characteristics.text: Bladder carcinoma
characteristics.characteristic: cell_subtype
characteristics.text: Epithelial cells
characteristics.characteristic: cell_type
characteristics.text: HT-1376 cells were seeded in T25 flasks overnight. The next day media was replaced with normal media without IFN (mock). Total RNA was prepared from cells 24 hrs post-treatment using the RNeasy Mini Kit (Qiagen). PolyA+ RNA was enriched from total RNA using the Dynabeads mRNA Purification Kit (Invitrogen). cDNA libraries were prepared from 200 ng of PolyA+ RNA using the Direct cDNA Sequencing Kit (Oxford Nanopore), according to the PCR-free 1D read protocol for full-length cDNA (Oxford Nanopore, SQK-DCS109), with some modifications. Specifically, RNase Cocktail Enzyme Mix (ThermoFisher) was used during the RNA digestion step after the first-strand synthesis; all reaction amounts for reverse transcription reactions up to the second-strand synthesis step were doubled; from second-strand synthesis up to adapter ligation, reactions were 1.5x of original amounts; during adapter ligation, 35 ul Blunt/TA Ligase Master Mix was used instead of the recommended 50 ul, and nuclease-free water was excluded. Final libraries were loaded into MinION Fluidics Module flow cells (Oxford Nanopore, FLO-MIN106D), and sequencing was carried out on GridION MK1 and MinION MK1C instruments (Oxford Nanopore) for 3 days, using default parameters.
characteristics.characteristic: description
characteristics.text: Carcinoma
characteristics.characteristic: disease
characteristics.text: Caucasian
characteristics.characteristic: ethnicity
characteristics.text: caucasian
characteristics.characteristic: isolate
characteristics.text: Homo sapiens
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: organism
characteristics.text: White
characteristics.characteristic: race
characteristics.text: female
characteristics.characteristic: sex
characteristics.text: Urinary bladder
characteristics.characteristic: tissue
characteristics.text: Human sample from Homo sapiens
characteristics.characteristic: title
characteristics.text: Mock
characteristics.characteristic: treatment