Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference |
Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Mus musculus) |
Stimulated by
retinoic acid 8 (Stra8) |
Mouse Genome Informatics | MGI:107917 | |
| Strain, strain background (M. musculus) |
B6 | Taconic | TAC: B6-F | C57BL/6NTac |
| Strain, strain background (M. musculus) |
B6/129 | Taconic | TAC: B6129-F | B6129F1/Tac |
| Strain, strain background (M. musculus) |
CD-1 | Charles River Laboratories | CRL: 022 | Crl:CD1(ICR) |
| Genetic reagent (M. musculus) |
Stra8FLAG | this paper | FLAG-tagged knock-in allelegenerated by CRISPR/Cas9 | |
| Genetic reagent (M. musculus) |
Stra8Δ121 | this paper | Stra8 allele with a121-bp deletion generated by CRISPR/Cas9 | |
| Genetic reagent (M. musculus) |
Stra8-deficient allele, Stra8- | The JacksonLaboratory | JAX: 023805; MGI:3622304 | Stra8tm1Dcp |
| Genetic reagent (M. musculus) |
Ddx4-Cre | PMID:23858447 | MGI:5554579 | Ddx4tm1.1(cre/mOrange)Dcp' |
| Genetic reagent (M. musculus) |
Rosa26-tdTomato | The Jackson Laboratory | JAX: 007914 | B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J |
| Cell line (M. musculus) |
v6.5 embryonic stem cells | other | RRID:CVCL_C865 | Jaenisch Lab, Whitehead Institute |
| Biological sample (M. musculus) |
CF6Neo Mouse Embryonic Fibroblasts (MEF), Mitomycin C Treated |
MTI-GlobalStem | GlobalStem:GSC-6105M | |
| Antibody | anti-STRA8 (rabbit polyclonal) |
Abcam | Abcam:ab49405; RRID:AB_945677 | (IF 1:250; IHC 1:500: WB 1:1000) |
| Antibody | anti-STRA8 (rabbit polyclonal) |
Abcam | Abcam:ab49602; RRID:AB_945678 | (IF 1:250; IHC 1:500: WB 1:1000) |
| Antibody | anti-FLAG M2 (mouse monoclonal) |
MilliporeSigma | MilliporeSigma:F1804; RRID:AB_262044 | (IHC 1:200) |
| Antibody | anti-FLAG M2, HRP-conjugated (mouse monoclonal) |
MilliporeSigma | MilliporeSigma:A8592; RRID: AB_439702 |
(WB 1:1000) |
| Antibody | anti-DMC1 H100 (rabbit polyclonal) |
Santa Cruz Biotechnology | SantaCruz:sc-22768; RRID:AB_2277191 | (IF 1:250) |
| Antibody | anti-SCP3 D-1 (mouse monoclonal) |
Santa CruzBiotechnology | SantaCruz:sc-74569; RRID:AB_2197353 | (IF 1:250) |
| Antibody | anti-phospho-histone H2AX (Ser139), clone JBW301 (mouse monoclonal) |
MilliporeSigma | MilliporeSigma:05–636; RRID:AB_309864 | (IF1:250) |
| Antibody | anti-DDX4/MVH (goat polyclonal) |
R and D Systems | R and D Systems:AF2030; RRID:AB_2277369 | (IF 1:500) |
| Antibody | anti-alpha tubulin, HRP-conjugated (rabbit polyclonal) |
Abcam | Abcam:ab40742; RRID:AB_880625 | (WB 1:5000) |
| Antibody | anti-goat Alexa Flour 488 (donkey polyclonal) |
JacksonImmunoResearch | JacksonImmunoResearch:705-546-147 | (IF 1:250) |
| Antibody | anti-rabbit Rhodamine Red-X (RRX) (donkey polyclonal) |
JacksonImmunoResearch | JacksonImmunoResearch:711-295-152 | (IF 1:250) |
| Antibody | anti-mouse Cy5 (donkey polyclonal) |
JacksonImmunoResearch | JacksonImmunoResearch:715-175-150 | (IF 1:250) |
| Antibody | anti-rabbit, peroxidase -conjugated (donkey polyclonal) |
JacksonImmunoResearch | JacksonImmunoResearch:711-035-152 | (WB 1:5000) |
| Recombinant DNA reagent |
pX330-U6-Chimeric_BB- CBh-hSpCas9 (plasmid) |
Addgene | Addgene:42230 | |
| Sequence- based reagent |
primers and oligonucleotides used in this study |
this paper | All primers and oligonucleotides used in this study are available in Supplementary file 6 |
|
| Chemical compound, drug |
N,N′-Octamethylenebis(2,2-dichloroacetamide) [Win18,446] |
Santa Cruz Biotechnology | SantaCruz:sc-295819 | |
| Chemical compound, drug |
Retinoic acid | MilliporeSigma | MilliporeSigma:R2625 | |
| Software, algorithm |
FASTX Toolkit | other | RRID:SCR_005534 | http://hannonlab.cshl.edu/fastx_toolkit/ |
| Software, algorithm |
Bowtie1 (v.1.2.0) | PMID:19261174 | RRID:SCR_005476 | http://bowtie-bio.sourceforge.net/index.shtml |
| Software, algorithm |
Samtools (v1.5) | PMID:19505943 | RRID:SCR_002105 | http://samtools.sourceforge.net/ |
| Software, algorithm |
MACS2 (v2.1.1.20160309) | PMID:18798982 | RRID:SCR_013291 | https://github.com/taoliu/MACS |
| Software, algorithm |
htseq count (v0.8.0) | PMID:25260700 | RRID:SCR_011867 | https://htseq.readthedocs.io |
| Software, algorithm |
kallisto (v0.43.0) | PMID:27043002 | RRID:SCR_016582 | https://pachterlab.github.io/kallisto/about |
| Software, algorithm |
DESeq2 (v1.18.1) | PMID:25516281 | RRID:SCR_015687 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Software, algorithm |
PANTHER (v13.1) | PMID:27899595 | RRID:SCR_004869 | http://www.pantherdb.org/ |
| Software, algorithm |
HOMER (v4.9.1) | PMID: 20513432 | RRID:SCR_010881 | http://biowhat.ucsd.edu/homer/index.html |
| Software, algorithm |
deepTools (v2.5.3) | PMID:27079975 | RRID:SCR_016366 | http://deeptools.readthedocs.io/en/latest/index.html |
| Software, algorithm |
RStudio v1.1.414 | RStudio | RRID:SCR_000432 | |
| Software, algorithm |
PHYLIP (v3.66) | Other | RRID:SCR_006244 | Distributed by J Felsenstein. http://evolution.genetics.washington.edu/phylip.html |
| Commercial assay or kit | Periodic Acid-Schiff (PAS) Kit | MilliporeSigma | MilliporeSigma:395B | |
| Commercial assay or kit | Mouse on Mouse ImmPRESS HRP (Peroxidase) Polymer Kit |
VECTOR Laboratories | VectorLabs:MP2400 | |
| Commercial assay or kit |
ImmPRESS HRP Anti-Rabbit IgG (Peroxidase) Polymer Detection Kit, made in Horse |
VECTOR Laboratories | VectorLabs:MP-7401 | |
| Commercial assay or kit |
mMESSAGE mMACHINE T7 Kit | Thermo Fisher Scientific |
ThermoFisher:AM1344 | |
| Commercial assay or kit |
MEGAshortscript T7 Kit | Thermo Fisher Scientific | ThermoFisher:AM1354 | |
| Commercial assay or kit |
MEGAclear Kit | Thermo Fisher Scientific | ThermoFisher:AM1908 | |
| Commercial assay or kit |
ChIP DNA Clean and Concentrator Kit |
Zymo Research | Zymo:D5205 | |
| Commercial assay or kit | TruSeq ChIP Sample Preparation Kit |
Illumina | Illumina:IP-202–1024 | |
| Commercial assay or kit | Accel-NGS 2S Plus DNA Library Kit |
Swift Biosciences | SwiftBio:21024 | |
| Commercial assay or kit |
TruSeq Stranded mRNA Library Prep Kit |
Illumina | Illumina:20020594 | |
| Other | Hematoxylin | Life Technologies | LifeTech:008011 | |
| Other | 2.5% Normal Horse Serum Blocking Solution |
VECTOR Laboratories | VectorLabs:S-2012 | |
| Other | ImmPACT DAB Peroxidase (HRP) Substrate |
VECTOR Laboratories | VectorLabs:SK-4105 | |
| Other | Normal donkey serum | Jackson ImmunoResearch | JacksonImmunoResearch:017000121 | |
| Other | VECTASHIELD Antifade Mounting Media for Fluorescence |
VECTOR Laboratories | VectorLabs:H-1000 | |
| Other | Collagenase, Type I | Worthington Biochemical |
Worthington:LS004196 | |
| Other | Hyaluronidase | MilliporeSigma | MilliporeSigma:H3506 | |
| Other | DNaseI | MilliporeSigma | MilliporeSigma:D5025 | |
| Other | Benzonase Nuclease | MilliporeSigma | MilliporeSigma:70664–3 | |
| Other | Protease inhibitor, EDTA Free | MilliporeSigma | MilliporeSigma: 11836170001 |
|
| Other | ESGRO Recombinant Mouse LIF Protein |
MilliporeSigma | MilliporeSigma:ESG1107 | |
| Other | Dynabeads Protein G for Immunoprecipitation |
Thermo Fisher Scientific | ThermoFisher:10004D | |
| Other | Lumi-Light Western Blotting Substrate |
MilliporeSigma | MilliporeSigma:12015200001 | |
| Other | DirectPCR Lysis Reagent (Mouse Tail) |
Viagen Biotech | Viagen:102 T |