characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2022-08-25T00:13:46Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2022-08-25T00:13:46Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA110653767
characteristics.characteristic: External Id
characteristics.text: South Australian Health and Medical Research Institute
characteristics.characteristic: INSDC center name
characteristics.text: 2022-08-25T00:13:46Z
characteristics.characteristic: INSDC first public
characteristics.text: 2022-08-25T00:13:46Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS12751349
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12020:Sample 23
characteristics.characteristic: Submitter Id
characteristics.text: 4
characteristics.unit: year
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: SH-SY5Y
characteristics.characteristic: cell_line
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: Tandem fluorescent LC3 (tf-LC3) constructs were created and the three cell lines (HeLa, HEK 293 and SH-SY5Y) were stably transformed as per Hein et al (10.1016/j.bbamcr.2017.06.011), creating tf-LC3 HeLa, tf-LC3 HEK 293 and tf-LC3 SH-SY5Y cell lines. HeLa and HEK 293 cells were cultured in Dulbecco's Modified Eagle Medium with 10% (v/v) foetal bovine serum and 5mg/mL penicillin and streptomycin in a humidified atmosphere of 5% carbon dioxide at 37 degrees Celcius. SH-SY5Y cells were cultured in 1:1 Dulbecco's Modified Eagle Medium:Ham's F12 Medium with 10% (v/v) foetal bovine serum and 5mg/mL penicillin and streptomycin in a humidified atmosphere of 5% carbon dioxide at 37 degrees Celcius. For mTOR experimental, cells cultured in appropriate growth medium (as per growth protocol) in T25 flasks until 80% confluent and were treated with the addition of 1 μM AZD8055 in DMSO for the specified time (0h, 1h, 15h, or 30h). For mTOR control, cells cultured in appropriate growth medium (as per growth protocol) in T25 flasks until 80% confluent and were treated with the addition of DMSO (vehicle) for the specified time (0h, 1h, 15h, or 30h). On completion of cell experiments, media was aspirated and cells were washed 3 times with cold PBS. Cells were harvested with trypsin which was inactivated by media and suspension was spun at 500g for 5 mins. Remaining media was aspirated and cell pellets were snap frozen until all experiments were completed, upon which time RNA was extracted from all samples concurrently. Total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN, Hilden North Rhine-Westphalia, Germany) as per the manufacturer’s instructions (sample RNA concentration ≥15 ng/μL, ≤2809 ng/μL, median 361.5 ng/μL). Standard Illumina protocol compatible with the NovaSeq 6000 sequencer.
characteristics.characteristic: description
characteristics.text: juvenile stage
characteristics.characteristic: developmental stage
characteristics.text: neuroblastoma
characteristics.characteristic: disease
characteristics.text: expressing tf-LC3
characteristics.characteristic: genotype
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: bone marrow
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: female
characteristics.characteristic: sex
characteristics.text: Sample 23
characteristics.characteristic: title