Appendix 1—key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Mus musculus, female) | Stag2+/− | This paper | Exon8 of Stag2 was targeted by CRISPR–Cas9 (see Materials and methods) |
|
| Strain, strain background (Mus. musculus, both sex) | Stag2f/y; Stag2f/f | This paper | Exon8 of Stag2 genomic locus was flanked by loxP sites (see Materials and methods) |
|
| Strain, strain background (Mus. musculus, both sex) | C57BL/6J | The Jackson Laboratory | 000664; RRID:IMSR_JAX:000664 |
|
| Strain, strain background (Mus. musculus, both sex) | B6.129-Gt(ROSA)26 Sortm1(cre/ERT2)Tyj/J |
The Jackson Laboratory | 008463; RRID:IMSR_JAX:008463 |
|
| Strain, strain background (Mus. musculus, male) | B6.Cg-Tg(Nes-cre)1Kln/J | The Jackson Laboratory | 003771; RRID:IMSR_JAX:003771 |
|
| Antibody | anti-STAG2 (Rabbit polyclonal) |
This paper | The C-terminus recombinant protein of STAG2 (Homo sapiens) was used to generate the antibody; WB (1:1000) |
|
| Antibody | anti-α-TUBULIN (Mouse monoclonal) |
Sigma-Aldrich | T9026; RRID:AB_477593 |
WB (1:1000) |
| Antibody | anti-SA1 (Rabbit polyclonal) |
Bethyl Laboratories | A302-579A; RRID:AB_2034857 |
WB (1:1000) |
| Antibody | anti-SMC1 (Rabbit polyclonal) |
Bethyl Laboratories | A300-055A RRID:AB_2192467 |
WB (1:1000) |
| Antibody | anti-SMC3 (Rabbit polyclonal) |
Bethyl Laboratories | A300-060A; RRID:AB_67579 |
WB (1:1000) |
| Antibody | anti-RAD21 (Rabbit polyclonal) |
Bethyl Laboratories | A300-080a; RRID:AB_2176615 |
WB (1:1000) |
| Antibody | anti-MBP (Rat monoclonal) |
Abcam | ab7349; RRID:AB_305869 |
IHC (1:100) |
| Antibody | anti-PLP1 (Rabbit polyclonal) |
Abcam | ab28486; RRID:AB_776593 |
IHC (1:100) |
| Antibody | anti-GFAP (Rabbit polyclonal) |
Abcam | ab7260; RRID:AB_305808 |
IHC (1:100) |
| Antibody | anti-MAP2 (Rabbit polyclonal) |
Abcam | ab32454; RRID:AB_776174 |
IHC (1:50) |
| Antibody | anti-H3K27ac (Rabbit polyclonal) |
Abcam | ab4729; RRID:AB_2118291 |
ChIP (5 μl per test) |
| Antibody | anti-O4 Microbeads (Mouse monoclonal) |
Miltenyi Biotec | 130-094-543; RRID:AB_2847907 |
MACS (10 μl per 107 cells) |
| Antibody | anti-rabbit IgG (H+L), DyLight 800 Conjugate (Goat polyclonal) | Cell Signaling Technology | 5151 S; RRID:AB_10697505 |
WB (1:5000) |
| Antibody | anti-mouse IgG (H+L), DyLight 680 Conjugate (Goat polyclonal) | Cell Signaling Technology | 5470 S; AB_10696895 |
WB (1:5000) |
| Antibody | anti-rat IgG (H+L), Alexa Fluor 568 (Goat polyclonal) | Thermo Fisher Scientific | A-11077; RRID:AB_2534121 |
IHC (1:500) |
| Antibody | anti-rabbit IgG (H+L), Alexa Fluor 488 (Goat polyclonal) | Thermo Fisher Scientific | A-11008; RRID:AB_143165 |
IHC(1:500) |
| Sequence-based reagent | sgRNA#1 target on Stag2 | This paper | CRISPR single-guide RNA target sequence |
Target sequence: TAGCCAACCTCTTTCTCTATTGG |
| Sequence-based reagent | sgRNA#2 target on Stag2 | This paper | CRISPR single-guide RNA target sequence |
Target sequence: CAGACAGTATACTGTAATGGAGG |
| Sequence-based reagent | TaqMan probes: Stag2 | Thermo Fisher Scientific | Mm01311611_m1 | |
| Sequence-based reagent | TaqMan probes: Klk6 | Thermo Fisher Scientific | Mm00478322_m1 | |
| Sequence-based reagent | TaqMan probes: Ninj2 | Thermo Fisher Scientific | Mm00450216_m1 | |
| Sequence-based reagent | TaqMan probes: Cpm | Thermo Fisher Scientific | Mm01250802_m1 | |
| Sequence-based reagent | TaqMan probes: Fa2h | Thermo Fisher Scientific | Mm00626259_m1 | |
| Sequence-based reagent | TaqMan probes: Gapdh | Thermo Fisher Scientific | Mm99999915_g1 | |
| Sequence-based reagent | Stag2 gt 5 F | This paper | Genotype sequence primers |
GGTATTTACTTGATAGCCAACC |
| Sequence-based reagent | Stag2 gt 5 R | This paper | Genotype sequence primers |
CTCATCTTGATTTTCCTGAAGC |
| Sequence-based reagent | Stag2 gt 3 F | This paper | Genotype sequence primers |
GGTTGAGACAGACAGTATAC |
| Sequence-based reagent | Stag2 gt 3 R | This paper | Genotype sequence primers |
AGGCTGGACTATGACAACTC |
| Sequence-based reagent | ISH Probe Stag2 P1 F | This paper | Riboprobe synthesis primers |
TACGGTACCGACCTTTCAGATGTCACTCCG |
| Sequence-based reagent | ISH Probe Stag2 P1 R | This paper | Riboprobe synthesis primers |
GAAGGATCCGCATCGGATAGACACTCATGA |
| Sequence-based reagent | ISH Probe Stag2 P2 F | This paper | Riboprobe synthesis primers |
TACGGATCCGACCTTTCAGATGTCACTCCG |
| Sequence-based reagent | ISH Probe Stag2 P2 R | This paper | Riboprobe synthesis primers |
GAAGGTACCGCATCGGATAGACACTCATGA |
| Sequence-based reagent | ISH Probe Stag1 P1 F | This paper | Riboprobe synthesis primers |
TTAGGTACCTTACAATGCCTGGTCCTCAGT |
| Sequence-based reagent | ISH Probe Stag1 P1 R | This paper | Riboprobe synthesis primers |
GAAGGATCCCTTTCATTGGCTCTCTTCCC |
| Sequence-based reagent | ISH Probe Stag1 P2 F | This paper | Riboprobe synthesis primers |
TTAGGATCCTTACAATGCCTGGTCCTCAGT |
| Sequence-based reagent | ISH Probe Stag1 P2 R | This paper | Riboprobe synthesis primers |
GAAGGTACCCTTTCATTGGCTCTCTTCCC |
| Commercial assay or kit | Arima-HiC Kit | Arima Genomics | 510008 | |
| Chemical compound, drug | Tamoxifen | Sigma-Aldrich | T5648 | |
| Chemical compound, drug | 4-Hydroxytamoxifen | Sigma-Aldrich | H7904 | |
| Software, algorithm | GraphPad Prism | GraphPad Software | RRID:SCR_002798; https://www.graphpad.com/scientific-software/prism/ |
|
| Software, algorithm | ImageJ (Fiji) | ImageJ | RRID:SCR_002285; https://imagej.net/software/fiji/ |
|
| Software, algorithm | RStudio | The R Foundation | RRID:SCR_000432; https://www.rstudio.com/ |
|
| Software, algorithm | Bcl2fastq | Illumina | RRID:SCR_015058 | v2.17 |
| Software, algorithm | Fastqc | Andrews, 2010; PMID:24501021 | RRID:SCR_014583 | v0.11.2 |
| Software, algorithm | Fastq_screen | Wingett, 2011 | RRID:SCR_000141; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
v0.4.4 |
| Software, algorithm | STAR | Dobin et al., 2013; PMID:23104886 | RRID:SCR_004463; https://github.com/alexdobin/STAR |
v2.5.3a |
| Software, algorithm | FeatureCounts | Liao et al., 2014; PMID:24227677 | RRID:SCR_012919; https://bioconductor.org/packages/release/bioc/html/Rsubread.html |
|
| Software, algorithm | edgeR | Robinson et al., 2010; PMID:19910308 | RRID:SCR_012802; https://bioconductor.org/packages/release/bioc/html/edgeR.html |
|
| Software, algorithm | Ingenuity pathway analysis | QIAGEN, Krämer et al., 2014; PMID:24336805 | RRID:SCR_008653; https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis | |
| Software, algorithm | MACS2 | Zhang et al., 2008; PMID:18798982 | RRID:SCR_013291 | v2.0.10 |
| Software, algorithm | Bowtie2 | Langmead and Salzberg, 2012; PMID:22388286 | RRID:SCR_016368 | v2.2.3 |
| Software, algorithm | Picard MarkDuplicates | Broad Institute, GitHub Repository | RRID:SCR_006525; http://broadinstitute.github.io/picard/ | v1.127 |
| Software, algorithm | HOMER | Heinz et al., 2010, Ross-Innes et al., 2012; PMID:20513432 | RRID:SCR_010881; http://homer.ucsd.edu/homer/ |
|
| Software, algorithm | Deeptools | Ramírez et al., 2016; PMID:27079975 | RRID:SCR_016366; https://deeptools.readthedocs.io/en/develop/ |
|
| Software, algorithm | Galaxy | Afgan et al., 2018; PMID:29790989 | RRID:SCR_006281; https://usegalaxy.org |
|
| Software, algorithm | Cell Ranger | 10× Genomics | RRID:SCR_017344; https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq |
|
| Software, algorithm | Seurat | New York Genome Center; Stuart et al., 2019; PMID:31178118 | RRID:SCR_016341; https://satijalab.org/seurat | Satija Lab |
| Software, algorithm | Monocle3 | UW Genome Sciences; Cao et al., 2019; PMID:30787437 | RRID:SCR_018685; https://cole-trapnell-lab.github.io/monocle3/ | Cole Trapnell’s Lab, v3.0 |
| Software, algorithm | HiC-Bench pipeline | Lazaris et al., 2017, Tsirigos et al., 2012; PMID:22113082 | https://github.com/NYU-BFX/hic-bench | v0.1 |
| Software, algorithm | Juicer ‘pre’ tool | Durand et al., 2016; PMID:27467249 | RRID:SCR_017226; https://github.com/aidenlab/juicer | Aiden Lab, v1.11.09 |
| Software, algorithm | Juicebox | Aiden Lab, BCM | RRID:SCR_021172; https://github.com/aidenlab/Juicebox | v1.5.1 |
| Software, algorithm | Hic2cool | Abdennur and Mirny, 2020; PMID:31290943 | https://github.com/4dn-dcic/hic2cool | v0.8.3 |
| Software, algorithm | pyGenomeTracks | Lopez-Delisle et al., 2021; PMID:32745185 | https://github.com/deeptools/pyGenomeTracks | v3.7 |
| Software, algorithm | Fit-HiC | Ay et al., 2014; PMID:24501021 | https://github.com/ay-lab/fithic | v2.0.7 |
| Software, algorithm | Coolpup.py | Flyamer et al., 2020; PMID:32003791 | https://github.com/open2c/coolpuppy | v0.9.5 |
| Software, algorithm | clusterProfiler | Bioinformatics Group, Southern Medical University; Wu et al., 2021; PMID:34557778 | RRID:SCR_016884; https://github.com/YuLab-SMU/clusterProfiler |
v4.4.1 |
| Software, algorithm | HiC-Pro | Servant et al., 2015; PMID:26619908 | RRID:SCR_017643 | v3.1.0 |
| Software, algorithm | HiCRep | Yang et al., 2017; PMID:28855260 | https://github.com/TaoYang-dev/hicrep | v1.11.0 |
| Software, algorithm | GENOVA | van der Weide et al., 2021; PMID:34046591 | https://github.com/robinweide/GENOVA | v1.0.0.9 |