KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit monoclonal anti-H3K27me3 | GeneTex | Cat#GTX60892 |
| Rabbit monoclonal anti-H2AK119ub | Cell Signaling | Cat#CST8240 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Recombinant mouse LIF | Sigma | Cat#ESG1107 |
| Critical Commercial Assays | ||
| NEBNext Poly(A) mRNA Magnetic Isolation Module | New England BioLabs | Cat#E7490S |
| Agencourt AMPure XP Beads | Beckman Coulter | Cat#A63881 |
| NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina | New England BioLabs | Cat#E6240S |
| NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) | New England BioLabs | Cat#E7335S |
| Quant-iT PicoGreen dsDNA Reagent | Thermo Fisher Scientific | Cat#P7581 |
| NEBNext Ultra Directional RNA Library Prep Kit for Illumina | New England BioLabs | Cat#E7420S |
| Deposited Data | ||
| RNA-seq in WT Xist female mouse differentiating ESC (days 0,5,6,7,8,10) | This study | GEO: GSE135389 |
| RNA-seq in WT Xist female mouse differentiating ESC (day 14) | Colognori et al., 2019 | GEO: GSE107217 |
| RNA-seq in ΔRepB Xist female mouse differentiating ESC (days, 0,5,6,7,8,10) | This study | GEO: GSE135389 |
| RNA-seq in ΔRepB Xist female mouse differentiating ESC (day 14) | Colognori et al., 2019 | GEO: GSE107217 |
| H3K27me3 ChIP-seq in WT Xist female mouse differentiating ESC (days 0,5,8,14) | This study | GEO: GSE135389 |
| H3K27me3 ChIP-seq in ΔRepB Xist female mouse differentiating ESC (days 0,5,8,14) | This study | GEO: GSE135389 |
| H2AK119ub ChIP-seq in WT Xist female mouse differentiating ESC (days 0,5,8,14) | This study | GEO: GSE135389 |
| H2AK119ub ChIP-seq in ΔRepB Xist female mouse differentiating ESC (days 0,5,8,14) | This study | GEO: GSE135389 |
| H3K27me3 ChIP-seq in WT Xist female MEF | Colognori et al., 2019 | GEO: GSE107217 |
| H3K27me3 ChIP-seq in ΔRepA Xist female MEF | This study | GEO: GSE135389 |
| H3K27me3 ChIP-seq in ΔRepB Xist female MEF | Colognori et al., 2019 | GEO: GSE107217 |
| H2AK119ub ChIP-seq in WT Xist female MEF | Colognori et al., 2019 | GEO: GSE107217 |
| H2AK119ub ChIP-seq in ΔRepA Xist female MEF | This study | GEO: GSE135389 |
| H2AK119ub ChIP-seq in ΔRepB Xist female MEF | Colognori et al., 2019 | GEO: GSE107217 |
| Mendeley data | This study | http://dx.doi.org/10.17632/77fjk9p346.1 |
| Experimental Models: Cell Lines | ||
| WT Xist female ESC (TsixTST/+) | Ogawa et al., 2008 | N/A |
| ΔRepA Xist female ESC (clone 8) | This study | N/A |
| ΔRepB Xist female ESC (clone D2) | Colognori et al., 2019 | N/A |
| ΔRepAB Xist female ESC (clone 9) | This study | N/A |
| WT Xist female MEF (EY.T4) | Yildirim et al., 2011 | N/A |
| “Old” ΔRepA Xist female MEF (clone X9) | Colognori et al., 2019 | N/A |
| “New” ΔRepA Xist female MEF (clone ds4) | This study | N/A |
| ΔRepB Xist female MEF (clone 22) | Colognori et al., 2019 | N/A |
| Oligonucleotides | ||
| Oligo FISH probes used for Xist RNA FISH | Colognori et al., 2019 | N/A |
| Stellaris FISH probes used for Atrx and Mecp2 nascent RNA FISH | LGC Biosearch Technologies | Custom |
| XMP X Green Mouse Chromosome Paint | MetaSystems | Cat#D-1420–050-FI |
| gRNAs used to generate Xist deletions (see Table S1) | Integrated DNA Technologies | N/A |
| PCR primers (see Table S2) | Integrated DNA Technologies | N/A |
| Recombinant DNA | ||
| pSpCas9(BB)-2A-GFP (PX461) | Ran et al., 2013 | Addgene Cat#48140 |
| pSpCas9(BB)-2A-Puro (PX459) v2.0 | Ran et al., 2013 | Addgene Cat#62988 |
| Software and Algorithms | ||
| HOMER v4.8 | Heinz et al., 2010 | http://homer.ucsd.edu/homer/index.html |
| NovoAlign v3.02 | Novocraft | http://www.novocraft.com/products/novoalign/ |
| TopHat2 v2.0.10 | Kim et al., 2013 | https://ccb.jhu.edu/software/tophat/index.shtml |
| SPP | Kharchenko et al., 2008 | http://compbio.med.harvard.edu/Supplements/ChIP-seq/ |
| featureCounts v1.5.0-p1 | Liao et al., 2014 | http://subread.sourceforge.net |
| SAMtools v1.4.1 | Li et al., 2009 | http://samtools.sourceforge.net/ |