Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference |
Identifiers | Additional information |
|---|---|---|---|---|
| Cell line (M. musculus, male) | Per2::lucSV EF | (Chen et al., 2012; Yoo et al., 2017) | Immortalized mouse ear fibroblast cells carrying PER2::LUCsv bioluminescence reporter | |
| Cell line (Human) | HEK293T | ATCC | CRL-3216 | |
| Cell line (M. musculus) | Per2::lucSV MEF | This paper | Primary mouse embryonic fibroblast cells carrying PER2::LUCsv bioluminescence reporter | |
| Cell line (M. musculus) | NIH3T3/E2LB | This paper | NIH3T3 cells carrying Per2 E-box (E2)-driven luciferase bioluminescence reporter | |
| Recombinant DNA reagent | pLKO.1-TRC | (Moffat et al., 2006) Addgene |
Plasmid #10878 | |
| Commercial assay or kit | RRBS kit | Diagenode | Cat#C02030033 | |
| Other | RNA-seq for all clonal cell lines | This paper | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132663 | |
| Other | RRBS-seq for 10 clonal cell lines | This paper | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132665 | |
| Other | Exome sequencing for clone#33 and #114 | This paper | https://www.ncbi.nlm.nih.gov/sra/PRJNA548837 | |
| Software, algorithm | FastQC | other | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | |
| Software, algorithm | TopHat | (Trapnell et al., 2009) | http://ccb.jhu.edu/software/tophat/index.shtml | |
| Software, algorithm | Samtools | (Li et al., 2009) | http://www.htslib.org/ | |
| Software, algorithm | HOMER | (Heinz et al., 2010) | http://homer.ucsd.edu/homer/ | |
| Software, algorithm | DESeq2 | (Love et al., 2014) | https://bioconductor.org/packages/release/bioc/html/DESeq2.html | |
| Software, algorithm | edgeR | (Robinson et al., 2010) | https://bioconductor.org/packages/release/bioc/html/edgeR.html | |
| Software, algorithm | featureCounts | (Liao et al., 2014) | http://bioinf.wehi.edu.au/featureCounts/ | |
| Software, algorithm | WGCNA | (Langfelder and Horvath, 2008) | https://cran.r-project.org/web/packages/WGCNA/index.html | |
| Software, algorithm | Trim Galore | other | https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ | |
| Software, algorithm | Bismark | (Krueger and Andrews, 2011) | https://www.bioinformatics.babraham.ac.uk/projects/bismark/ | |
| Software, algorithm | methylKit | (Akalin et al., 2012) | https://bioconductor.org/packages/release/bioc/html/methylKit.html | |
| Software, algorithm | STRING | (Szklarczyk et al., 2019) | https://string-db.org/ | |
| Software, algorithm | MeV | other |
https://sourceforge.
net/projects/mev-tm4/ |
|
| Software, algorithm | ggplot2 | (Wickham, 2016) | https://github.com/tidyverse/ggplot2 | |
| Software, algorithm | qqman | (Turner, 2014) | https://github.com/stephenturner/qqman | |
| Software, algorithm | dplyr | (Wickham et al., 2018) |
https://dplyr.tidyverse.org
|
|
| Software, algorithm | Ingenuity Pathway Analysis | Qiagen | https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis | |
| Software, algorithm | ImageJ2 (Fiji) with trackmate | NIH | https://imagej.net/ImageJ2 | |
| Software, algorithm | BioVenn | (Hulsen et al., 2008) | http://www.biovenn.nl/ | |
| Software, algorithm | Prism | GraphPad Software | https://www.graphpad.com/scientific-software/prism/ |