Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference |
Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Escherichia coli) | BL21(DE3) | Thermo Scientific | Cat No. C600003 | Competent cells |
| Cell line (Homo sapiens) | HEK-293T | ATCC | Cat No. CRL-3216 | The cell line is commercially available at ATCC |
| Cell line (Homo sapiens) | HEK-293 | ATCC | Cat No. CRL-1573 | The cell line is commercially available at ATCC |
| Cell line (Homo sapiens) | TREx BCBL1-Rta | A gift of JU Jung (University of Southern California, USA). | Nakamura et al., 2003 | |
| Cell line (Homo sapiens) | BCBL1 | A gift from Dr Andrew Hislop (University of Birmingham, UK). | Renne et al., 1996 | |
| Antibody | Anti-m6A (rabbit polyclonal) | Merck Millipore | ABE572 | m6A-seq and m6A-IP |
| Antibody | Anti-SND1 (rabbit polyclonal) | Proteintech | 10760–1-AP | WB (1:1,000). 2 µg for RIP-seq and RIP 2 µg per ChIP |
| Antibody | Anti-SND1 (mouse monoclonal) | Proteintech | 60265–1-Ig | WB (1:1,000). |
| Antibody | Anti-FXR1 (rabbit polyclonal) | Proteintech | 13194–1-AP | 2 µg per RIP |
| Antibody | Anti-FXR2 (rabbit polyclonal) | Proteintech | 12552–1-AP | 2 µg per RIP |
| Antibody | Anti-PSIP1 (rabbit polyclonal) | Proteintech | 25504–1-AP | 2 µg per RIP |
| Antibody | Anti-METTL3 (rabbit polyclonal) | Bethyl laboratories | A301-567A | WB (1:500) |
| Antibody | Anti-FTO (rabbit monoclonal) | Abcam | ab126605 | WB (1:5,000) |
| Antibody | Anti-YTHDF1 (rabbit polyclonal) | Proteintech | 17479–1-AP | WB (1:1,000) 1 µg per RIP |
| Antibody | Anti-YTHDF2 (rabbit polyclonal) |
Abclonal | A9639 | WB (1:500) |
| Antibody | Anti-YTHDF3 (rabbit polyclonal) |
Abclonal | A8395 | WB (1:500) 5.8 µg per RIP |
| Antibody | Anti-ORF57 (mouse monoclonal) | Santa Cruz | sc-135746 | WB (1:1,000) |
| Antibody | Anti-RTA (rabbit polyclonal) |
A gift from Professor David Lukac (Rutgers, New Jersey, USA) |
Lukac et al., 1998 | WB (1:1,000) |
| Antibody | Anti-ORF54 (mouse monoclonal) | A gift from Friedrich Grässer (University of Homburg, Germany) | Kremmer et al., 1999 | WB (1:1,000) |
| Recombinant DNA reagent | FLAG-ORF50 plasmid (pCDH-CMV-MCS-EF1-Puro) for mammalian expression | NovoPro Bioscience | Custom made. | Purchased from NovoPro, available upon request from the Whitehouse laboratory. |
| Recombinant DNA reagent | GST-SND1-C-terminus (residues 548–910) for bacteria expression |
NovoPro Bioscience | Custom made. | Purchased from NovoPro, available upon request from the Whitehouse laboratory. |
| Recombinant DNA reagent | GST-FXR1-plant agenet (residues 2–132) for bacteria expression | NovoPro Bioscience | Custom made. | Purchased from NovoPro, available upon request from the Whitehouse laboratory. |
| Recombinant DNA reagent | GST-PSIP1-PWWP (residues 3–100) for bacteria expression |
NovoPro Bioscience | Custom made. | Purchased from NovoPro, available upon request from the Whitehouse laboratory. |
| Recombinant DNA reagent | GST-CBX3-Chromo (residues 29–86) for bacteria expression | NovoPro Bioscience | Custom made. | Purchased from NovoPro, available upon request from the Whitehouse laboratory. |
| Sequence-based reagent | Mission TRC shRNA SND1 KD1 | Sigma | TRCN0000245143 | Mission TRC shRNA bacterial glycerol stock commercially available from Sigma |
| Sequence-based reagent | Mission TRC shRNA SND1 KD2 | Sigma | TRCN0000049656 | Mission TRC shRNA bacterial glycerol stock commercially available from Sigma |
| Commercial assay or kit | RNA fragmentation reagent | Thermo Scientific | AM8740 | |
| Commercial assay or kit | Pierce chromatin prep module | Thermo Scientific | 26158 | |
| Commercial assay or kit | LightShift chemiluminescent RNA EMSA Kit | Thermo Scientific | 20158 | |
| Commercial assay or kit | EZ-ChIP | Merck Millipore | 17–371 | |
| Commercial assay or kit | DNA-free DNA Removal Kit | Thermo Scientific | AM1906 | |
| Chemical compound, drug | 3-deazaadenosine (DAA) | Cambridge Bioscience | 9000785–5 mg | |
| Software, algorithm | m6aViewer 1.6 software | dna2.leeds.ac.uk/m6a/ | Antanaviciute et al., 2017 | Published in the RNA journal. 2017 Oct; 23(10): 1493–1501. |
| Other | Magna ChIP Protein A+G magnetic beads | Merck Millipore | 16–663 | Used for m6A-seq and RIP-seq |