Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (mouse) | Hbs1lGTC | This study (see Materials and methods) |
MMRRC #007694-UCD; RRID:MMRRC007694-UCD | International Gene Trap Consortium, IGTC, cell line ID: XE494 |
| Strain, strain background (mouse) | Hbs1ltm1a(C57BL/6N-Atm1BrdHbs1ltm1a(KOMP)Wtsi) | Skarnes et al., 2011 | MMRRC #048037-UCD, RRID:MMRRC048037-UCD | |
| Strain, strain background (mouse) | B6N.129S4-Gt(ROSA)26Sortm1(FLP1)Dym/J | The Jackson Laboratory | JAX:016226; RRID:IMSRJAX:016226 | |
| Strain, strain background (mouse) | B6N.Cg-Edil3Tg(Sox2-Cre)1Amc/J | The Jackson Laboratory | JAX:014094; RRID:IMSRJAX:014094 | |
| Strain, strain background (mouse) | B6.FVB-Tg(EIIa-Cre)C5379Lmgd/J | The Jackson Laboratory | JAX:003724; RRID:IMSRJAX:003724 | |
| Strain, strain background (mouse) | En1tm2(Cre)Wrst/J | The Jackson Laboratory | JAX:007916; RRID:IMSRJAX:007916 | |
| Strain, strain background (mouse) | B6.Cg-Tg(Atoh1-Cre)1Bfri/J | The Jackson Laboratory | JAX:011104; RRID:IMSRJAX:011104 | |
| Strain, strain background (mouse) | B6.Cg-Tg(CAG-Cre/Esr1*)5Amc/J | JAX:004682; RRID:IMSRJAX:004682 | ||
| Strain, strain background (mouse) | B6.Tg(Gabra6-Cre)B1Lfr | Fünfschilling and Reichardt, 2002 | N/A | |
| Strain, strain background (mouse) | B6J-Pelofl/fl | This study (see Materials and methods) |
N/A | |
| Strain, strain background (mouse) | Upf2fl/fl | Weischenfeldt et al., 2008 | N/A | |
| Strain, strain background (mouse) | B6J.B6Nn-Tr20 | Ishimura et al., 2014 | N/A | |
| Strain, strain background (mouse) |
B6J-n-Tr20-/- | Ishimura et al., 2016 | N/A | |
| Antibody | Anti-phospho-eIF2alphaS51
(Rabbit polyclonal) |
Cell Signaling Technology | CST #9721; RRID:AB_330951 |
WB (1:1000) |
| Antibody | Anti-eIF2alpha (Rabbit polyclonal) |
Cell Signaling Technology | CST #9722; RRID:AB_2230924 |
WB (1:2000) |
| Antibody | Anti-phospho-p70S6KT389
(Rabbit monoclonal) |
Cell Signaling Technology | CST #9234; RRID:AB_2269803 |
WB (1:1000) |
| Antibody | Anti-p70S6K (Rabbit monoclonal) |
Cell Signaling Technology | CST #2708; RRID:AB_390722 |
WB (1:1000) |
| Antibody | Anti-phospho-S6S240/244
(Rabbit monoclonal) |
Cell Signaling Technology | CST #5364; RRID:AB_10694233 |
IF (1:1000) |
| Antibody | Anti-cleaved caspase 3 (Rabbit polyclonal) |
Cell Signaling Technology | CST #9661; RRID:AB_2341188 |
IF (1:100) |
| Antibody | Anti-BrdU (Mouse monoclonal) |
Dako/Agilent | M0744; RRID:AB_10013660 |
IF (1:50) |
| Antibody | Anti-Hbs1l (Rabbit polyclonal) |
Proteintech | #10359–1-AP; RRID:AB_2114730 |
WB (1:1000) |
| Antibody | Anti-Pelo (Rabbit polyclonal) |
Proteintech | #10582–1-AP; RRID:AB_2236833 |
WB (1:2000) |
| Antibody | Anti-Vinculin (Mouse monoclonal) |
Sigma-Aldrich | V9131; RRID:AB_477629 | WB (1:20,000) |
| Antibody | Anti-GAPDH (Rabbit monoclonal) |
Cell Signaling Technology | CST #2118; RRID:AB_561053 |
WB (1:10,000) |
| Antibody | Anti-Ki67 (Rabbit Polyclonal) |
Abcam | ab15580; RRID:AB_443209 |
IF (1:100) |
| Antibody | Anti-Olig2 (Rabbit monoclonal) |
Abcam | ab109186; RRID:AB_10861310 |
IF (1:200) |
| Antibody | Anti-Lhx1/5 (Mouse monoclonal) |
DSHB | #4F2-c; RRID:AB_531784 |
IF (1:100) |
| Antibody | Anti-NeuN (Mouse monoclonal) |
Millipore | MAB377; RRID:AB_2298772 |
IF (1:500) |
| Antibody | Anti-Tbr1 (Rabbit polyclonal) |
Millipore | AB9616; RRID:AB_2200223 |
IF (1:1000) |
| Antibody | Anti-Pax2 (Rabbit polyclonal) |
Thermo Fisher Scientific | #71–6000; RRID:AB_2533990 |
IF (1:50) |
| Antibody | Anti-pH3 (Rabbit polyclonal) | Upstate, Millipore | #06–570; RRID:AB_310177 | IF (1:1000) |
| Antibody | Anti-PCNA (Mouse monoclonal) |
Invitrogen, Thermo Fisher Scientific | MA5-11358; RRID:AB_10982348 |
IF (1:100) |
| Chemical compound, drug | DNase I | Worthington | LS002139 | |
| Chemical compound, drug | Bromodeoxyuridine (BrdU) | Sigma-Aldrich | B9285 | |
| Chemical compound, drug | 5-Bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-Gal) | Sigma-Aldrich | B4252 | |
| Chemical compound, drug | Z-4-hydroxytamoxifin (4OHT) | Sigma-Aldrich | H7905 | |
| Commercial assay or kit | RNAscope Multiplex Fluorescent Reagent Kit v2 | Advanced Cell Diagnostics | #323100 | |
| Commercial assay or kit | KAPA Stranded mRNA-seq. Kit | Roche | KR0960 | |
| Commercial assay or kit | iQ SYBR Green Supermix | Bio-Rad | #1708880 | |
| Commercial assay or kit | SuperScript III First-Strand Synthesis System | Invitrogen | #18080051 | |
| Commercial assay or kit | DNA-free DNA Removal Kit | Life Technologies | AM1906 | |
| Commercial assay or kit | TSA Plus Cyanine 3 | PerkinElmer | NEL744001KT | |
| Other | RNA-seq. and ribosome profiling data | This study (see Materials and methods) |
GSE162556 | Deposited Data |
| Sequence-based reagent | Hbs1l GTC (Genotyping) | This study (see Materials and methods) |
N/A | Common Forward:5’AGTCCAGGTGTTTCCTCACG3’; Wild type Reverse:5’CCCTGGCCTATTTTTGGTTT3’; GTC Reverse:5’TGTCCTCCAGTCTCCTCCAC3’ |
| Sequence-based reagent | Hbs1l cKO (Genotyping) | This study (see Materials and methods) |
N/A | Forward I: 5’CATGGCCTCCTATGGGTTGA3’; Forward II: 5’GCCTACAGTGAGCACAGAGT3’; Reverse: 5’TAGGTGCTGGGATTTGAACC3’ |
| Sequence-based reagent | Pelo cKO (Genotyping) | This study (see Materials and methods) |
N/A | Forward:5’TGTAACTGAACCCTGCAGTATCT3’; Reverse I: 5’GTGGAGCATGAAATGAAATTCGG3’; Reverse II: 5’ATCCAAGGCTTTTACTTCGCC3’ |
| Sequence-based reagent | RNAscope probe Hbs1l-C2 | Advanced Cell Diagnostics | #527471-C2 | |
| Sequence-based reagent | Hbs1l Exon 3–6 (RT-PCR) | This study (see Materials and methods) |
N/A | Forward Primer:5’GAAATTGACCAAGCTCGCCTGTA3’; Reverse Primer:5’CTCAGAAGTTAAGCCAGGCACT3’ |
| Sequence-based reagent | β-actin (RT-PCR) | Terrey et al., 2020 | N/A | Forward Primer:5’GGCTGTATTCCCCTCCATCG3’; Reverse Primer:5’CCAGTTGGTAACAATGCCATGT3’ |
| Sequence-based reagent | Hbs1l Isoform I (quantitative RT-PCR) | This study (see Materials and methods) |
N/A | Forward Primer:5’AGACCATGGGATTTGAAGTGC3’; Reverse Primer:5’CCGGTCTCAGGAATGTTAGGA3’ |
| Sequence-based reagent | Hbs1l Isoform II (quantitative RT-PCR) | This study (see Materials and methods) |
N/A | Forward Primer:5’TGAAGTTGAACAAAGTGCCAAG 3’; Reverse Primer:5’CTGCTTCCTCTGTGTTCCTC3’ |
| Sequence-based reagent | Pelo (quantitative RT-PCR) | This study (see Materials and methods) |
N/A | Forward Primer:5’CCCCAGGAAACGGAAAGGC3’; Reverse Primer:5’ACGCACTTTACAACCTCGAAG3’ |
| Sequence-based reagent | Gapdh (quantitative RT-PCR) | Ishimura et al., 2016 | N/A | Forward Primer:5’CATTGTCATACCAGGAAATG3’; Reverse Primer:5’GGAGAAACCTGCCAAGTATG3’ |
| Software, algorithm | Image J | NIH | RRID:SCR_003070; https://imagej.nih.gov/ij | |
| Software, algorithm | GraphPad Prism 7 | GraphPad Prism | RRID:SCR_002798 | |
| Software, algorithm | Pause site identification algorithm | Ishimura et al., 2014 | N/A | |
| Software, algorithm | biomaRt version 2.42.1 | Durinck et al., 2005 | RRID:SCR_019214; https://bioconductor.org/packages/release/bioc/html/biomaRt.html | |
| Software, algorithm | ShinyGO v0.61 (KEGG pathway) | Ge et al., 2020 | RRID:SCR_019213; http://bioinformatics.sdstate.edu/go | |
| Software, algorithm | Ingenuity Pathway Analysis (IPA) | QIAGEN Inc | RRID:SCR_008653; https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis | |
| Software, algorithm | DESeq2 v1.26.0 | Love et al., 2014 | RRID:SCR_015687; https://bioconductor.org/packages/release/bioc/html/DESeq2.html | |
| Software, algorithm | ensembldb v2.6.8 | Rainer et al., 2019 | RRID:SCR_019103; https://www.bioconductor.org/packages/release/bioc/html/ensembldb.html | |
| Software, algorithm | riborex v2.3.4 | Li et al., 2017 | RRID:SCR_019104; https://github.com/smithlabcode/riborex | |
| Software, algorithm | RiboWaltz v1.0.1 | Lauria et al., 2018 | RRID:SCR_016948; https://github.com/LabTranslationalArchitectomics/RiboWaltz | |
| Software, algorithm | bowtie2 v 2.2.3 | Langmead and Salzberg, 2012 | RRID:SCR_005476; http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | |
| Software, algorithm | fastx_trimmer | Hannon Lab | http://hannonlab.cshl.edu/fastx_toolkit/ | |
| Software, algorithm | fastx_clipper | Hannon Lab | http://hannonlab.cshl.edu/fastx_toolkit/ | |
| Software, algorithm | hisat2 v2.1.0 | Kim et al., 2019 | RRID:SCR_015530;https://daehwankimlab.github.io/hisat2/ | |
| Software, algorithm | featureCounts | Liao et al., 2014 | RRID:SCR_012919; http://bioinf.wehi.edu.au/featureCounts | |
| Software, algorithm | sleuth v0.30.0 | Pimentel et al., 2017 | RRID:SCR_016883;https://pachterlab.github.io/sleuth/about | |
| Software, algorithm | kallisto v0.42.4 | Bray et al., 2016 | RRID:SCR_016582;https://pachterlab.github.io/kallisto/about |