characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2022-02-04T00:14:26Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2022-02-04T00:14:26Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA12561572
characteristics.characteristic: External Id
characteristics.text: Department of Pathology,the First Affiliated Hospital of Soochow University
characteristics.characteristic: INSDC center name
characteristics.text: 2022-02-04T00:14:26Z
characteristics.characteristic: INSDC first public
characteristics.text: 2022-02-04T00:14:26Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS10168104
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-11321:YTHDF3-HCT116_input_2
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: HCT116
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0002824
characteristics.characteristic: cell line
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: HCT116 cells were cultured within Dulbecco's Modified Eagle Medium (DMEM) with 10% fetal bovine serum (FBS). HCT116 cells were long-term cultured within DMEM containing 10% FBS and 1 μg/mL oxaliplatin. 1×107 cells were harvested, resuspended in nuclear isolation buffer (1.28 M sucrose, 40 mM Tris pH 7.5, 20 mM MgCl2, 4% Triton X-100) and kept on ice for at least 30 min with frequent mixing. The pellet nuclei were centrifuged with 14000 rpm for 15 min, resuspended by wash buffer (150 mM KCl, 25 mM Tris pH 7.4, 5 mM EDTA, 0.5 mM DTT, 0.5% NP40, 100 U/mL RNAase inhibitor (Solarbio, Beijing, China), 1×Protease inhibitors cocktail (Solarbio) and sheared the chromatin through sonication by high power, 5 s on, 30 s off for 30 cycles. After that, 90% nuclei were incubated with 1 μg antibodies of m6A methylation (Cat No. 56593S, CST, Beverly, USA), YTHDF3, eIF3A (Cat No. NBP1-18891, NOVUS, Centennial, USA) or eIF2AK2 overnight and 40 μL Protein A/G beads (Thermo Fisher Scientific) 2 h by gentle rotation at 4 °C while the rest of 10% were harvested as input. The pellet beads were centrifuged by 3000 rpm 3 min, washed three times. Both the input and pellet beads were purified by RNAiso plus (Takara, Kusatsu, Japan) and conducted reverse transcription using QuantiTect Reverse Transcription Kit (Qiagen, Hilden, Germany). Libraries of cDNA were used for next generation sequencing or qPCR. For sequencing, the concentration and quality of purified RIP RNAs was measured by Nanodrop 2000 (Thermo Fisher Scientific) and Agilent bioanalyzer 2100 (Agilent, Santa Clara, USA). 4 μg RNA in each group were used for library preparation by NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) following manufacturer’s instructions
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: colorectal cancer
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0005842
characteristics.characteristic: disease
characteristics.text: wild type genotype
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0005168
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: large intestine
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0000059
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: YTHDF3-HCT116_input_2
characteristics.characteristic: title