characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-09-01T05:28:43Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-09-01T05:28:43Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA113425355
characteristics.characteristic: External Id
characteristics.text: Center for Omics Sciences IRCCS San Raffaele Scientific Institute
characteristics.characteristic: INSDC center name
characteristics.text: 2023-09-01T05:28:43Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-09-01T05:28:43Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS15420482
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12953:HCT116_FOLFIRI_LT_2
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: HCT116
characteristics.characteristic: cell_line
characteristics.text: colorectal cancer cell
characteristics.characteristic: cell_type
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: Cells were trypsinized, harvested and washed with PBS/0.04% BSA and immediately used. HCT116 cells were grown in DMEM supplemented with 10% Fetal Bovine Serum Cells were plated, and after 24h were treated with FOLFOX or FOLFIRI at the following concentration: 5-FU 100µM + OXA 100µM (FOLFOX) or 5-FU 100µM + SN-38 100nM (FOLFIRI) for 8h or 16h. Then, cells were harvested for experimental purposes. For long term (2 weeks) treatments, cells were plated and exposed to 5-FU 10µM + OXA 1µM (FOLFOX) or 5-FU 10µM + SN-38 10nM (FOLFIRI). Nucleic acids were directly processed on permeabilized nuclei following the “Nuclei Isolation for Single Cell ATAC Sequencing” protocol CG000169, Rev D (10X Genomics). Specifically, we prepared the nuclei suspension in order to get 5’000 nuclei as target nuclei recovery. Single-cell GET-seq was performed on Chromium platform (10x Genomics) following “Chromium Single Cell ATAC Reagent Kits” user manual version CG000168 Rev C. Tn5 and TnH were used in substitution of the 10X ATAC enzyme (10X Genomics) in the transposition mix assembly step. When a sequential Tn5 to TnH reaction was performed, a transposition mix containing 1.5 uL of Tn5 was incubated 30 min at 37 °C, then 1.5 uL of TnH was added and the reaction was continued for a total of 1 h incubation.
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: colorectal carcinoma
characteristics.characteristic: disease
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: intestine
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: male
characteristics.characteristic: sex
characteristics.text: HCT116_FOLFIRI_LT_2
characteristics.characteristic: title