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. Author manuscript; available in PMC: 2025 Apr 18.
Published in final edited form as: Mol Cell. 2024 Mar 7;84(8):1442–1459.e7. doi: 10.1016/j.molcel.2024.02.013

Key resources table

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Primary Ab-SYCP3 Abcam ab97672
Alexa Fluor 488 Goat anti-Mouse IgG Thermo Fisher Scientific A-21121
Bacterial and virus strains
Biological samples
WT C57BL/6J (P) × CAST/EiJ (M) F1 mouse embryo This paper N/A
WT CAST/EiJ (P) × C57BL/6J (M) F1 mouse embryo This paper N/A
XistXm/- female mouse embryo This paper N/A
Chemicals, peptides, and recombinant proteins
Acid Tyrode’s solution Sigma-Aldrich Cat#T1788-100ML
acetylated BSA Sigma-Aldrich Cat#B8894-5ML
RNase inhibitor Roche Cat#3335399001
DTT Thermo Fisher Scientific Cat#P2325
ATP New England BioLabs Cat#P0756S
Betaine SIGMA-ALDRICH Cat#B0300-5VL
Biotin-14-CTP Thermo Fisher Scientific Cat#19519-016
RLT plus buffer Qiagen Cat#1053393
Unmethylated lambda DNA Promega Cat#D1521
4-Thiouridine Sigma-Aldrich Cat#T4509-25MG
Iodoacetamide (IAA) Sigma-Aldrich Cat#I1149-5G
Cy3-dUTP Enzo life Sciences Cat#enz-42501
Aminoallyl-dUTP-XX-AF647 Jena BioScience Cat#NU-803-XX-AF647-S
Tergitol Sigma-Aldrich Cat#NP40S-100ML
Ribonucleoside-vanadyl complex New England BioLabs Cat#S1402S
Critical commercial assays
Agencourt AMPure XP Beads Beckman Coulter Cat# A63881
Streptavidin C1 beads Thermo Fisher Scientific Cat#65001
Nextera XT DNA library preparation kit Illumina Cat#FC-131-1024
Nextera XT Index Kit Illumina Cat#FC-131-1001
Kapa high fidelity PCR mix Kapa Biosystems Cat# KK2601
EZ methylation kit Zyon Cat# D5020
PureLink PCR Purifiation kit Thermo Fisher Scientific Cat#K310001
Qubit dsDNA Quantification Assay Kit Thermo Fisher Scientific Cat#Q32851
Deposited data
Single embryo So-Smart-seq, 4SU-RNAseq, Bisulfite- DNAseq and bulk RNA-seq data This paper GSE168455
Early embryo Hi-C data Du et al.46 GSE82185
Early embryo H3K27me3 ChIP-seq data Zheng et al.60 GSE76687
Early embryo ATAC-seq data Wu et al.65 GSE66390
Male germline single-cell RNAseq Chen et al.66 GSE107644
Sperm ATAC-seq Jung et al.67 GSE79230
Experimental models: Cell lines
Mouse: ES cell line: TsixTST/+ Ogawa et al.84 N/A
Experimental models: Organisms/strains
Mouse: C57BL/6J: WT Jackson Laboratory Cat#000664
Mouse: CAST/EiJ: WT Jackson Laboratory Cat#000928
Mouse: 129S1/SvlmJ: Xist−/Y Marahrens et al.32 N/A
Oligonucleotides
Reverse-dT Primers for So-smart-seq: TTTCCCTACACGACGCTCTTCCGATCTNNNNNNTTTTTTTTTTTTTTTVVN This paper N/A
GGrG oligo
iCiGiCGGAGTTCAGACGTGTGCTCTTCCGATCTrGrG+G		 This paper N/A
Library PCR forward primer: GTGACTGGAGTTCAGACGTGTGCTCTTC This paper N/A
Library PCR reverse primer: ACACTCTTTCCCTACACGACGCTCTTC This paper N/A
oligo-dT for Alkylation-dependent RNAseq: /5Biotin-TEG/AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN Hendriks et al.44 N/A
ISPCR Reverse primer: AAGCAGTGGTATCAACGCAGAGT Hendriks et al.44 N/A
NEBNext Multiplex Oligos for Illumina New England BioLabs E7335S
Oligos for ribosomal cDNA depletion (see Table S5) This paper N/A
Short oligo probes for FISH experiments (see Table S6) This paper N/A
Nextera XT Index Kit Illumina Cat#FC-131-1001
Recombinant DNA
Software and algorithms
edgeR Robinson et al.89 N/A
Trim Galore Babraham Bioinformatics Group N/A
STAR Dobin et al.87 N/A
RepeatMasker Smit et al.91 N/A
featureCounts Liao et al.88 N/A
sam2tsv Lindenbaum92 N/A
Novoalign Novocraft N/A
DeepTools Ramirez et al.93 N/A
Bismark Krueger et al.94 N/A
Rstudio Posit N/A
SingleCellExperiment Amezquita et al.95 N/A
scran Lun et al.96 N/A
pheatmap https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf N/A
NbClust Charrad et al.97 N/A
gridExtra https://cran.r-project.org/web/packages/gridxtra/index.html N/A
ggplot2 Wickham98 N/A
IGV Thorvaldsdottir et al.90 N/A
R scripts for the plots generated in this paper This paper doi:10.7910/DVN/W7RJFI
Other