Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Mus musculus) | Vsx2 | Ensembl: ENSMUSG00000021239 |
||
| Strain, strain background (Mus musculus. male and female) | CD-1 | Charles River | Strain code 022 | |
| Genetic reagent (Mus musculus) | Otx2-GFP | Fossat et al., 2007 | ||
| Genetic reagent (Mus musculus) | Grm6-YFP | Morgan et al., 2011 | ||
| Genetic reagent (Mus musculus) | Otx2-GFP;Grm6-YFP | This paper | Cross between Otx2-GFP and Grm6-YFP | |
| Recombinant DNA reagent | pCAGGS | Hsiau et al., 2007 | Plasmid used to create Gnb3 reporters. | |
| Recombinant DNA reagent | Gnb3-WT-DsRed | This paper | Gnb3 promoter region driving DsRed | |
| Recombinant DNA reagent | Gnb3-WT-EGFP | This paper | Gnb3 promoter region driving EGFP | |
| Recombinant DNA reagent | Gnb3- K50 #1-null-DsRed- | This paper | ||
| Recombinant DNA reagent | Gnb3- K50 #2-null-DsRed- | This paper | ||
| Recombinant DNA reagent | Gnb3- K50 #3-null-DsRed- | This paper | ||
| Recombinant DNA reagent | Gnb3- K50 #4-null-DsRed- | This paper | ||
| Recombinant DNA reagent | Gnb3- K50 #5-null-DsRed- | This paper | ||
| Recombinant DNA reagent | Gnb3- K50 #3 and #5-null-DsRed- | This paper | ||
| Recombinant DNA reagent | Gnb3- Q50 #1-EGFP | This paper | ||
| Recombinant DNA reagent | Gnb3- Q50 #3-EGFP | This paper | ||
| Recombinant DNA reagent | Gnb3- Q50 #1 and #3-EGFP | This paper | ||
| Commercial assay or kit | Qiagen Mini-elute PCR Purification kit | Qiagen | Cat no. 28004 | |
| Commercial assay or kit | KAPA Library Quantification Kit | Roche | Cat no. 07960140001 | |
| Commercial assay or kit | SMARTer Ultra Low RNA kit for Illumina Sequencing-HV | Clonetech | Cat. Nos. 634820, 634823, 634826, 634828 and 634830) | Utilized by Washington University Genome Technology Access Core (GTAC) |
| Sequence-based reagent | Primers | IDT | Listed in Supplementary file 2 | |
| Software, algorithm | R | http://rstudio.com | R programming language | |
| Software, algorithm | DESeq2 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html | Differential gene expression analysis based on the negative binomial distribution | |
| Software, algorithm | HOMER | http://homer.ucsd.edu/homer/index.html | Hypergeometric Optimization of Motif EnRichment | |
| Software, algorithm | SAMtools | http://www.htslib.org | Samtools | |
| Software, algorithm | Bowtie2 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | Bowtie2 | |
| Software, algorithm | Picard | https://broadinstitute.github.io/picard/ | Picard | |
| Software, algorithm | MACS2 | https://pypi.org/project/MACS2/2.1.1.20160309/ | Model-based Analysis of ChIP-Seq | |
| Software, algorithm | STAR | https://github.com/alexdobin/STAR | Spliced Transcripts Alignment to a Reference | |
| Software, algorithm | HTSeq | https://pypi.org/project/HTSeq/ | HTSeq |