characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-09-22T00:22:02Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-09-22T00:22:02Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA111432181
characteristics.characteristic: External Id
characteristics.text: Institute for Research on Cancer and Aging, Nice (IRCAN) Inserm U1081 - CNRS UMR 7284
characteristics.characteristic: INSDC center name
characteristics.text: 2023-09-22T00:22:02Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-09-22T00:22:02Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS13525856
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12240:AZA_1
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: HCT116
characteristics.characteristic: cell_line
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: HCT-116 cells were cultured in McCoy medium supplemented with 10% FBS, 100 U/mL penicillin and 100 µg/mL streptomycin. For 5-aza-2'-deoxycytidine (DAC) treatment, cells were plated at a density of 100,000 cells/well in 6-well plates and treated with DAC at a final concentration of 1 μM for a total of 5 days. Fresh medium and drug were added daily for the first 3 days. In control samples (mock), 5-aza was replaced by DMSO. Genomic DNA was extracted and prepared using QiaAmp DNA Blood mini kit (Qiagen) In brief, bs-ATLAS-seq follows these steps: fragmentation of genomic DNA by sonication, ligation of a methylated adapter, bisulfite treatment of linker-ligated DNA, suppression PCR-amplification of L1 5' junctions, and asymmetric Illumina paired-end sequencing (90 bp + 210 bp). Read #1 starts from a random position (sonicated DNA break), while read #2 starts from a fixed sequence in L1 5' UTR (internal promoter). With this design, read #2 covers the 15 most 5’ CpG sites (1-207, relative to L1HS consensus sequence). Read #1 has the same orientation as the L1 element.
characteristics.characteristic: description
characteristics.text: colorectal carcinoma
characteristics.characteristic: disease
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: mixed large intestine and colon
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: AZA_1
characteristics.characteristic: title