|
Antibodies
|
| Rabbit monoclonal anti-alpha-Tubulin (EP1332Y) |
Abcam |
Cat# ab52866 RRID: AB_869989 |
| Mouse Anti-Dnmt3a Monoclonal Antibody, Clone 64B1446 |
Abcam |
Cat# ab13888 RRID: AB_300714 |
| IRDye 800CW Goat anti-Rabbit IgG antibody |
LI-COR Biosciences |
Cat# 926-32211 RRID: AB_621843 |
| IRDye 800CW Goat anti-Mouse IgG antibody |
LI-COR Biosciences |
Cat# 926-32210 RRID: AB_621842 |
| Rabbit polyclonal anti-Histone H3 (acetyl K27) |
Abcam |
Cat# ab4729 RRID: AB_2118291 |
|
Bacterial and Virus Strains
|
|
Chemicals, Peptides, and Recombinant Proteins
|
|
Critical Commercial Assays
|
| Mspa1I |
NEB |
Cat# R0577 |
| AllPrep DNA/RNA Kit |
QIAGEN |
Cat# 80284 |
| Ovation Ultralow Methyl-Seq Kit |
Tecan |
Cat# 0335-32 |
| Epitect Bisulfite Kit |
Qiagen |
Cat# 59824 |
| EZ DNA Methylation-Direct Kit |
Zymo Research Corporation |
Cat# D5020 |
| Accel-NGS Methyl-Seq DNA Library Kit |
Swift Biosciences |
Cat# 30024 |
| NEBNext Ultra Directional RNA Library Prep Kit for Illumina |
NEB |
Cat# E7420 |
| NEBNext rRNA Depletion Kit (Human/Mouse/Rat) |
NEB |
Cat# E6310 |
| Accel-NGS 2S Plus DNA Library Kit (24 rxns) |
Swift Biosciences |
Ca# 21024 |
|
Oligonucleotides
|
|
Actb Forward |
IDT |
AAGGCCAACCGTGAAAAGAT |
|
Actb Reverse |
IDT |
GTGGTACGACCAGAGGCATAC |
|
Dnmt3a Forward |
IDT |
GGCCTT CTCGACTCCAGATG |
|
Dnmt3a Reverse |
IDT |
TTCCTCTTCTCAGCTGGCAC |
|
Dnmt3a P900L Region Forward |
IDT |
AGAGGGGCATTTATGGATGA |
|
Dnmt3a P900L Region Reverse |
IDT |
GAGGGGCCTATTTTGCTTTT |
|
Recombinant DNA
|
|
Deposited data
|
| RNA-sequencing data |
This paper |
GEO: GSE225372
|
| ChIP-sequencing data (H3K27ac) |
This paper |
GEO: GSE225372
|
| Bisulfite-sequencing data |
This paper |
GEO: GSE225372
|
| Bisulfite-sequencing data |
(Lister et al., 2013) |
GEO: GSE47966
|
| RNA-, ChIP-, and Bisulfite-sequencing data |
(Clemens et al., 2019) |
GEO: GSE123373
|
| RNA-sequencing data |
(Christian et al., 2020) |
GEO: GSE147899
|
| RNA-sequencing data |
(Hamagami et al., 2023) |
GEO: GSE212847
|
| Mus musculus mm9 genome assembly |
UCSC |
http://hgdownload.soe.ucsc.edu/goldenPath/mm9/
|
| Ensembl gene models |
UCSC |
https://genome.ucsc.edu/cgi-bin/hgTables
|
|
Experimental models: organisms/strains
|
| C57BL/6J |
The Jackson Laboratory |
JAX:000664 |
| Dnmt3a P900L/+ |
This paper |
|
| Dnmt3a R878H/+ |
(Smith et al. 2021) |
Provided by T. Ley |
|
Experimental models: cell lines
|
|
Software and Algorithms
|
| DESeq2 (v1.14.1) |
(Love et al., 2014) |
http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
|
| edgeR (v3.16.5) |
(Robinson et al., 2009) |
https://bioconductor.org/packages/release/bioc/html/edgeR.html
|
| SAMtools (v1.3) |
(Li and Durbin, 2009) |
https://sourceforge.net/projects/samtools/files/
|
| BEDtools2 (v2.25.0) |
(Quinlan and Hall, 2010) |
https://github.com/arq5x/bedtools2
|
| Bowtie2 (v2.2.5) |
(Langmead and Salzberg, 2012) |
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
| STAR |
(Dobin et al., 2013) |
https://github.com/alexdobin/STAR
|
| fastQC |
|
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
|
| Trim galore |
|
https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
|
| BS-seeker2 |
(Guo et al., 2013) |
https://github.com/BSSeeker/BSseeker2
|
| BSmooth |
(Hansen et al., 2012) |
https://www.bioconductor.org/packages/release/bioc/html/bsseq.html
|
| ImageJ |
|
https://imagej.nih.gov/ij/
|
| GraphPad Prism v9.4.1 |
|
https://www.graphpad.com/
|
| Avizo |
|
http://www.vsg3d.com/
|
| ITK-SNAP |
|
http://itksnap.org/
|
| PANTHER Gene Ontology (v17.0) |
|
http://www.pantherdb.org/tools/compareToRefList.jsp
|
| RRHO2 |
(Cahill et al., 2018); (Plaisier et al., 2010) |
https://github.com/RRHO2/RRHO2
|
