Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Mus musculus) |
Norad (2900097C17Rik) | NA | Ensembl: ENSMUSG00000102869 |
|
| Gene (Homo sapiens) |
NORAD (LINC00657) | NA | Ensembl: ENSG00000260032 |
|
| Genetic reagent (Mus musculus) |
Norad-/- mice | This paper; see Materials and methods section Generation of mice with Norad deletion or enforced PUM2 expression |
||
| Genetic reagent (Mus musculus) |
Pum2 (TRE-FLAG-Pum2) mice |
This paper; see Materials and methods section Generation of mice with Norad deletion or enforced PUM2 expression |
||
| Genetic reagent (Mus musculus) |
rtTA3 (CAG-rtTA3) mice | The Jackson Laboratory | Stock# 016532 | |
| Genetic reagent (Mus musculus) |
C57BL/6J mice | UTSW Breeding Core | ||
| Cell line (Mus musculus) |
Norad-/- primary MEFs | This paper; see Materials and methods section Generation and culture of mouse embryonic fibroblasts (MEF) |
||
| Cell line (Mus musculus) |
Norad+/- primary MEFs | This paper; see Materials and methods section Generation and culture of mouse embryonic fibroblasts (MEF) |
||
| Cell line (Mus musculus) |
Norad+/+ primary MEFs | This paper; see Materials and methods section Generation and culture of mouse embryonic fibroblasts (MEF) |
||
| Cell line (Mus musculus) |
Norad-/- immortalized MEFs |
This paper; see Materials and methods section Generation and culture of mouse embryonic fibroblasts (MEF) |
||
| Cell line (Mus musculus) |
Norad+/+ immortalized MEFs |
This paper; see Materials and methods section Generation and culture of mouse embryonic fibroblasts (MEF) |
||
| Cell line (Mus musculus) |
rtTA3 primary MEFs | This paper; see Materials and methods section Generation and culture of mouse embryonic fibroblasts (MEF) |
||
| Cell line (Mus musculus) |
Pum2 primary MEFs | This paper; see Materials and methods section Generation and culture of mouse embryonic fibroblasts (MEF) |
||
| Cell line (Mus musculus) |
Pum2;rtTA3 primary MEFs |
This paper; see Materials and methods section Generation and culture of mouse embryonic fibroblasts (MEF) |
||
| Cell line (Mus musculus) |
Neuro-2a | ATCC | CCL-131 | |
| Cell line (Mus musculus) |
CT26 | ATCC | CRL-2638 | |
| Cell line (Mus musculus) |
Hepa1-6 | ATCC | CRL-1830 | |
| Cell line (Homo sapiens) |
HCT116 | ATCC | CCL-247 | |
| Cell line (Homo sapiens) |
NORAD-/- HCT116 | Lee et al. (2016) | ||
| Cell line (Homo sapiens) |
PUM1 OE HCT116 | Lee et al. (2016) | ||
| Cell line (Homo sapiens) |
PUM2 OE HCT116 | Lee et al. (2016) | ||
| Antibody | Anti-PUM2 (polyclonal goat) |
Santa Cruz | sc-31535 | eCLIP |
| Antibody | Anti-PUM2 (monoclonal rabbit) |
Abcam | ab92390 | WB (1:4000) |
| Antibody | Anti-PUM1 (monoclonal rabbit) |
Abcam | ab92545 | WB (1:4000) |
| Antibody | Anti-GAPDH (monoclonal rabbit) |
Cell Signaling | #2118 | WB (1:5000) |
| Antibody | Anti-FLAG (polyclonal rabbit) |
Cell Signaling | #2368 | WB (1:1000) |
| Antibody | IRDye 800CW anti-rabbit (donkey) |
Licor | 925–32213 | WB (1:10000) |
| Antibody | Anti-FLAG M2 (monoclonal mouse) |
Sigma-Aldrich | F1804 | IHC |
| Antibody | Anti-4-HNE (polyclonal rabbit) |
Abcam | ab46545 | IHC |
| Antibody | Anti-DNA/RNA Damage (monoclonal mouse) |
Abcam | ab62623 | IF |
| Antibody | Anti-Digoxigenin (monoclonal mouse) | Roche | 11333062910 | RNA FISH |
| Antibody | Anti-Mouse IgG, Cy3 (polyclonal goat) |
EMD Millipore | AP124C | RNA FISH |
| Recombinant DNA reagent |
pTRE-Tight-FLAG-Pum2 | This paper; see Materials and methods section Generation of mice with Norad deletion or enforced PUM2 expression |
||
| Recombinant DNA reagent |
pCAG-FLAG-Pum2 | This paper; see Materials and methods section FLAG-PUM2 overexpression in MEFs |
||
| Recombinant DNA reagent |
pcDNA3-EGFP | This paper; see Materials and methods section FLAG-PUM2 overexpression in MEFs |
||
| Recombinant DNA reagent |
pX330-U6-Chimeric_BB- CBh-hSpCas9 |
Addgene | #42230 | |
| Sequence-based reagent |
Mouse IDetect Point Probe Chr. 2 (red) |
Empire Genomics | IDMP1002-R | DNA FISH |
| Sequence-based reagent |
Mouse IDetect Point Probe Chr. 16 (green) |
Empire Genomics | IDMP1016-1-G | DNA FISH |
| Sequence-based reagent |
Norad (2900097C17Rik) TaqMan assay |
Applied Biosystems | Mm04242407_s1 | qPCR |
| Sequence-based reagent |
NORAD custom TaqMan assay |
Lee et al. (2016) | N/A | qPCR |
| Commercial assay or kit |
Total ROS ID Detection Kit |
Enzo Life Sciences | ENZ-51011 | |
| Commercial assay or kit |
3-nitrotyrosine (3-NT) ELISA |
Mybiosource | MBS262795 | |
| Chemical compound, drug |
Tetramethylrhodamine ethyl ester (TMRE) | Enzo Life Sciences | ENZ-52309 | |
| Software, algorithm | Prism 7 | GraphPad Software | ||
| Software, algorithm | NGS QC Toolkit (v2.3.3) | Patel and Jain, 2012 | ||
| Software, algorithm | Tophat2 (v2.0.12) | Kim et al., 2013 | ||
| Software, algorithm | HISAT2 (v2.1.0) | Pertea et al., 2016 | ||
| Software, algorithm | FeatureCount (v1.4.6) and (v1.6.0) |
Liao et al. (2014) | ||
| Software, algorithm | EdgeR (v3.8.6) and (v3.24.0) |
Robinson et al. (2010) | ||
| Software, algorithm | Stringtie (v1.2.2) | Pertea et al., 2015 | ||
| Software, algorithm | BEDtools | Quinlan and Hall (2010) | ||
| Software, algorithm | Gene set enrichment analysis |
Subramanian et al. (2005) | ||
| Software, algorithm | Database for Annotation, Visualization and Integrated Discovery (DAVID) |
Huang et al., 2009a |