| Gene (Mus musculus) |
Ddx3x
|
NA |
MGI:103064; NCBI Gene: 13,205 |
|
| Gene (M. musculus) |
Ddx3y
|
NA |
MGI:1349406; NCBI Gene: 26,900 |
|
| Gene (M. musculus) |
Rcor2
|
NA |
MGI:1859854; NCBI Gene: 104,383 |
|
| Gene (M. musculus) |
Setd3
|
NA |
MGI:1289184; NCBI Gene: 52,690 |
|
| Gene (M. musculus) |
Topbp1
|
NA |
MGI:1920018; NCBI Gene: 235,559 |
|
| Genetic reagent (M. musculus) |
C57BL/6 J |
Jackson Laboratory |
JAX #000664; RRID:IMSR_JAX:000664
|
|
| Genetic reagent (M. musculus) |
Emx1-Cre |
Jackson Laboratory |
JAX #005628; RRID:IMSR_JAX:005628; MGI:2684610 |
MGI symbol: Emx1 tm1(cre)Krj |
| Genetic reagent (M. musculus) |
Rosa26Ai14
|
Jackson Laboratory |
JAX #007914; RRID:IMSR_JAX:007914
|
MGI symbol: Gt(ROSA)26Sor tm14(CAG-tdTomato)Hze |
| Genetic reagent (M. musculus) |
Neurod6-Cre (NEX-Cre) |
PMID:17146780
|
MGI:2668659 |
MGI symbol: Neurod6 tm1(cre)Kan |
| Genetic reagent (M. musculus) |
Ddx3xlox/lox
|
PMID:27179789
|
MGI:5774968 |
MGI symbol: Ddx3x tm1.1Lyou |
| Genetic reagent (M. musculus) |
Ddx3y sgRNAs |
this paper |
NCBI gene: 26,900 |
generated with Benchling for depleting Ddx3y; see Figure 2
|
| Genetic reagent (M. musculus) |
smFISH probes for Ddx3x
|
this paper |
NCBI gene: 13,205 |
generated with script from Tsanov et al., 2016 for monitoring Ddx3x RNA; see Figure 1
|
| Genetic reagent (M. musculus) |
Scrambled siRNAs |
Qiagen |
Qiagen:1022076 |
|
| Genetic reagent (M. musculus) |
Setd3 siRNAS |
Qiagen |
Qiagen:1027416 |
Gene ID: 52,690 |
| Cell line (M. musculus, male) |
Neuro-2a |
ATCC |
ATCC:CCL-131; RRID:CVCL_0470
|
|
| Strain, strain background |
NEB 5-alpha Competent E. coli (High Efficiency) |
New England Biolabs |
NEB:C2987H |
|
| Sequence-based reagent (M. musculus) |
Rcor2 qPCR primers |
Harvard PrimerBank; PMID:22086960
|
|
Harvard PrimerBank ID: 154147710 c2; Forward 5'-TGCTTCTGTGGCATAAACACG-3'; Reverse 5'-GGCTGGGAATCACCTTGTCAG-3' |
| Sequence-based reagent (M. musculus) |
Setd3 qPCR primers |
Harvard PrimerBank; PMID:22086960
|
|
Harvard PrimerBank ID: 21312266a1; Forward 5'-AAATCAGGTACTGGGGCTACA-3'; Reverse 5'-GGCCCATTTCATTAGATCAGGGA-3' |
| Sequence-based reagent (M. musculus) |
Topbp1 qPCR primers |
Harvard PrimerBank; PMID:22086960
|
|
Harvard PrimerBank ID: 118130322 c1; Forward 5'-CAGGATTGTTGGTCCTCAAGTG-3'; Reverse 5'-ACAGGATACAGTTACGTCAGACA-3' |
| Antibody |
anti-SOX2 (rat monoclonal) |
ThermoFisher |
ThermoFisher:14-9811-82; RRID:AB_11219471
|
(1:1000) |
| Antibody |
anti-BrdU (rat monoclonal) |
Abcam |
Abcam:ab6326 |
(1:200) |
| Antibody |
anti-TUJ1 (mouse monoclonal) |
Biolegend |
Biolegend:801202; RRID:AB_10063408
|
(1:2000) |
| Antibody |
anti-CTIP2 (rat monoclonal) |
Abcam |
Abcam:AB18465 |
(1:500) |
| Antibody |
anti-TBR2 (rabbit polyclonal) |
Abcam |
Abcam:AB23345; RRID:AB_778267
|
(1:1000) |
| Antibody |
anti-CC3 (rabbit polyclonal) |
Cell Signaling |
Cell Signaling:9661; RRID:AB_2341188
|
(1:250) |
| Antibody |
anti-NEUROD2 (rabbit polyclonal) |
Abcam |
Abcam:AB104430; RRID:AB_10975628
|
(1:500) |
| Antibody |
anti-Ki67 (rabbit monoclonal) |
Cell Signaling Technology |
Cell Signaling:12,202 |
(1:1000) |
| Antibody |
anti-PH3 (rabbit polyclonal) |
Millipore |
Millipore:06–570 |
(1:500) |
| Antibody |
anti-TBR1 (rabbit monoclonal) |
Cell Signaling Technology |
Cell Signaling Technology:49,661 S |
(1:1000) |
| Antibody |
anti-DDX3X (rabbit polyclonal) |
Sigma Aldrich |
Sigma Aldrich:HPA001648; RRID:AB_1078635
|
(IF, 1:500; western, 1:1000) |
| Antibody |
anti-GFP (chicken polyclonal) |
Abcam |
Abcam:Ab13970; RRID:AB_300798
|
(1:1000) |
| Antibody |
anti-B-actin (mouse monoclonal) |
Santa Cruz |
Santa Cruz:sc-47778 |
(1:500) |
| Antibody |
anti-mouse HRP (goat polyclonal) |
ThermoFisher |
ThermoFisher:32430; RRID:AB_1185566
|
(1:2000) |
| Antibody |
anti-rabbit HRP (goat polyclonal) |
ThermoFisher |
ThermoFisher:A16110; RRID:AB_2534782
|
(1:2000) |
| Antibody |
anti-GFP (mouse monoclonal) |
Santa Cruz |
Santa Cruz:sc9996 |
|
| Antibody |
AlexaFluor-conjugated secondary antibodies (488, 555, 568, 594, 647) |
ThermoFisher |
|
(1:500) |
| Recombinant DNA reagent |
pX330-U6-Chimeric_BB-CBh-hSpCas9 |
Addgene |
AddGene:42230; RRID:Addgene_42230
|
|
| Recombinant DNA reagent |
pX330-U6-Chimeric_BB-CBh-hSpCas9+Ddx3y guides |
this paper |
|
Cloned for depletion of Ddx3y; see Figure 2
|
| Recombinant DNA reagent |
pCAG-GFP |
PMID:32135084
|
|
|
| Recombinant DNA reagent |
pCAG-GFP-human DDX3X |
PMID:32135084
|
|
|
| Commercial assay or kit |
Click-it EdU AlexaFluor 594 imaging kit |
Life Technologies |
Life Technologies:c10339 |
|
| Commercial assay or kit |
Qiagen RNAeasy kit |
Qiagen |
Qiagen:74,034 |
|
| Commercial assay or kit |
Qiagen miRNA library prep kit |
Qiagen |
Qiagen:331,502 |
|
| Commercial assay or kit |
RiboMinus Eukaryote kit v2 |
ThermoFisher |
ThermoFisher:A15020 |
|
| Commercial assay or kit |
RNA Analysis Kit (15 nt) |
Agilent |
Agilent:DNF-471 |
|
| Commercial assay or kit |
Kapa mRNA HyperPrep kit with mRNA capture |
KapaBiosystems |
KapaBiosystems:KR1352 |
|
| Commercial assay or kit |
iScript cDNA synthesis kit |
BioRad |
BioRad:1708891 |
|
| Commercial assay or kit |
iTaq Universal Sybr Green Supermix |
BioRad |
BioRad:1725121 |
|
| Commercial assay or kit |
BCA protein quantification |
ThermoFisher |
ThermoFisher:23,227 |
|
| Commercial assay or kit |
ECL |
ThermoFisher |
ThermoFisher:32,106 |
|
| Chemical compound, drug |
EdU |
ThermoFisher |
ThermoFisher:A10044 |
|
| Chemical compound, drug |
BrdU |
Sigma Aldrich |
Sigma:B5002 |
|
| Chemical compound, drug |
Cycloheximide |
Calbiochem |
Sigma:239,764 |
|
| Software, algorithm |
Fiji/ImageJ |
PMID:22743772
|
|
v1.52i |
| Software, algorithm |
QuPATH |
PMID:29203879
|
|
v0.3.2 |
| Software, algorithm |
bowtie2 |
PMID:22388286
|
|
v2.4.4 |
| Software, algorithm |
STAR |
PMID:23104886
|
|
v2.7.9a |
| Software, algorithm |
RibosomeProfilingQC |
DOI:10.18129/B9.bioc.ribosomeProfilingQC
|
|
v1.8.0 |
| Software, algorithm |
Ribo-seQC |
DOI:10.1101/601468
|
|
v0.99 |
| Software, algorithm |
DESeq2 |
PMID:25516281
|
|
v1.34.0 |
| Software, algorithm |
ORFquant |
PMID:33765284
|
|
v1.02 |
| Software, algorithm |
R |
R Foundation for Statistical Computing |
|
v4.1.0 |
| Other |
Vectashield |
Vector Labs |
Vector Labs:H-1000–10 |
See immunoflourescence section in methods |
| Other |
DAPI stain |
ThermoFisher |
ThermoFisher:D1306 |
See FACS section in methods |
| Other |
Propidium iodide stain |
ThermoFisher |
ThermoFisher:P3566 |
See FACS section in methods |
| Other |
Hoechst stain |
ThermoFisher |
ThermoFisher:H3570 |
See immunoflourescence section in methods |
| Other |
Turbo DNase I |
Invitrogen |
Invitrogen:AM2238 |
See RNAseq and ribosome footprinting section in methods |
| Other |
Superase In |
Invitrogen |
Invitrogen:AM2694 |
See RNAseq and ribosome footprinting section in methods |
| Other |
TRIzol |
Invitrogen |
Invitrogen:15596026 |
See RNAseq and ribosome footprinting section in methods |
| Other |
GlycoBlue |
Invitrogen |
Invitrogen: AM9515 |
See RNAseq and ribosome footprinting section in methods |
| Other |
PNK enzyme |
New England Biolabs |
NEB:M0247S |
See RNAseq and ribosome footprinting section in methods |
| Other |
15% acrylamide denaturing urea-gel |
BioRad |
BioRad:4566053 |
See RNAseq and ribosome footprinting section in methods |
| Other |
2 X sample dye |
Novex |
Novex:LC6876 |
See RNAseq and ribosome footprinting section in methods |
| Other |
dsDNA ladder |
ThermoFisher |
ThermoFisher:10488023 |
See RNAseq and ribosome footprinting section in methods |
| Other |
miRNA ladders |
New England Biolabs |
NEB:N2102S |
See RNAseq and ribosome footprinting section in methods |
| Other |
SYBR gold |
Invitrogen |
Invitrogen:S11494 |
See RNAseq and ribosome footprinting section in methods |
| Other |
SpinX column |
Corning |
Corning:CLS8162 |
See RNAseq and ribosome footprinting section in methods |
| Other |
TRIzol LS reagent |
ThermoFisher |
ThermoFisher:10296010 |
See RNA Immunoprecipitation section in methods |
| Other |
Lipofectamine 2000 |
ThermoFisher |
ThermoFisher:11668019 |
See RNA Immunoprecipitation section in methods |
| Other |
Protein G-coated Dynabeads |
ThermoFisher |
ThermoFisher:0003D |
See RNA Immunoprecipitation section in methods |
| Other |
GoTaq Green Master Mix |
Promega |
Promega:M712 |
See RNA Immunoprecipitation section in methods |
| Other |
1 X RIPA buffer |
Pierce |
Pierce:89,900 |
See SDS-PAGE and western blot analysis section in methods |
| Other |
2 X sample buffer |
BioRad |
BioRad:1610737 |
See SDS-PAGE and western blot analysis section in methods |
| Other |
protease inhibitors |
Sigma Aldrich |
Sigma:78,429 |
See SDS-PAGE and western blot anlaysis section in methods |
| Other |
12% polyacrylamide gel |
BioRad |
BioRad:4568046 |
See SDS-PAGE and western blot anlaysis section in methods |
| Other |
PVDF membrane |
BioRad |
Biorad:1704157 |
See SDS-PAGE and western blot anlaysis section in methods |
