Anti ybx1 antibody

The ChIP assay was performed using the BeyoChIP™ ChIP Assay Kit (Beyotime, Shanghai, China) according to the manufacturer’s instructions. Briefly, 1 × 10⁷ CRC cells were prepared and then cross-linked with 1% formaldehyde for 15 min at room temperature. The cross-linking process was quenched by adding 0.125 M glycine. Chromatin was isolated with the lysis buffer provided in the kit. Afterwards, sonication was performed to shear the DNA to 200–1000 bp. Immunoprecipitation of cross-linked protein/DNA was performed by incubating anti-YBX1 antibody (Proteintech, IL, USA) or normal rabbit IgG (Proteintech, IL, USA) with sheared chromatin overnight at 4 °C followed by incubation with Protein A/G Magnetic Beads for 2 h. Subsequently, cross-links of protein/DNA were released with 5 M NaCl, and the DNA was purified using a PCR Clean Up Kit (Beyotime, Shanghai, China). Finally, the purified DNA was subjected to qRT–PCR using the P1-P9 primer sequences listed in Additional file 1: Table S4.

Cells were lysed with NETN buffer on ice for 20 min and then centrifuged at 12,000 rpm for 20 min to extract proteins. Then, the proteins were separated by SDS-PAGE. The following antibodies were used: anti-CDKL1 antibody (Abcam, ab136129), anti-YBX1 antibody (Proteintech, 20339-1-AP), anti-GAPDH antibody (Proteintech, 60,004-I-Ig), anti-Flag-tag antibody (ABclonal, AE005), anti-Myc-tag antibody (ABclonal, AE010), anti-H3 antibody (Proteintech, 17168-1-AP), anti-α-tubulin antibody (Proteintech, 11224-1-AP), and anti-PD-L1 antibody (Proteintech, 17952-1-AP).