Skip to main content
. Author manuscript; available in PMC: 2024 Mar 16.
Published in final edited form as: Cell. 2023 Mar 16;186(6):1162–1178.e20. doi: 10.1016/j.cell.2023.02.023

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Histone H3.3 G34R RevMab 31-1120, RRID:AB_2716433
Histone H3.3 G34V RevMab 31-1193, RRID:AB_2716435
Histone H3.3 G34W RevMab 31-1145 RRID:AB_2716434
H3K27me3 Cell Signaling Technology 9733, RRID:AB_2616029
H3K27ac Diagenode C15410196, RRID:AB_2637079
H3K36me3 Active Motif 61021, RRID:AB_2614986
H3K36me2 Active Motif 39255
DNMT3A Abcam Ab2850
FLAG Cell Signaling Technology 8146
Total H3 Abcam Ab1791
Calbindin Millipore Sigma C9848
Iba1 Abcam Ab178846, Ab283346
NeuN Millipore Sigma MAB377
GFAP Cell signalling 12389S
Oct6 Millipore Sigma MABN738
C1q Abcam Ab182451
C3 Novus Biologicals NB200-540
PSD95 Abcam Ab18258
NF200 Millipore Sigma N4142
Bacterial and Virus Strains
Biological Samples
Chemicals, Peptides, and Recombinant Proteins
Recombinant Cas9 IDT
Critical Commercial Assays
Deposited Data
WGBS, ChIP-seq, bulk RNA-seq, single nuceli RNA-seq & ATAC-seq data for murine samples This paper GEO: GSE199885 reviewer token: ohybqqkabbmbzcp
Experimental Models: Cell Lines
C3H10T1/2 o/e FLAG-HA-H3.3 WT Jain et al., 2020 N/A
C3H10T1/2 o/e FLAG-HA-H3.3 G34R Jain et al., 2020 N/A
C3H10T1/2 o/e FLAG-HA-H3.3 G34W Jain et al., 2020 N/A
U2-OS FlpIn-T-Rex o/e GFP-FLAG-BIoID2 This paper N/A
U2-OS FlpIn-T-Rex o/e NLS-GFP-FLAG-BIoID2 This paper N/A
U2-OS FlpIn-T-Rex o/e H3.3-WT-FLAG-BIoID2 This paper N/A
U2-OS FlpIn-T-Rex o/e H3.3-G34R-FLAG-BIoID2 This paper N/A
U2-OS FlpIn-T-Rex o/e H3.3-G34V-FLAG-BIoID2 This paper N/A
U2-OS FlpIn-T-Rex o/e H3.3-G34W-FLAG-BIoID2 This paper N/A
DKI H3.3 G34R NPC This paper N/A
DKI H3.3 G34V NPC This paper N/A
DKI H3.3 G34W NPC This paper N/A
Experimental Models: Organisms/Strains
Mouse: B6C3F1/Crl Charles River Laboratories RRID:IMSR_CRL:031
Mouse: C57BL/6J The Jackson Laboratory RRID:IMSR_JAX:000 664
Oligonucleotides
H3f3a exon 2 targeting sgRNA TAGAAATACCTGTAACGATG This paper N/A
H3f3a intron 1 targeting gRNA CGCGCTGGCAACGAGCGACT This paper N/A
H3f3a G34R ssODN
CCGCAAATCCACCGGTGGTAAAGCACCCAGGAAAC
AACTGGCTACAAAAGCCGCTCGCAAGAGTGCGCCC
TCTACTGGAAGGGTGAAGAAACCTCACCGCTATAG
GTATTTCTAAAACGTCGAGCAGTGGGATAGTGTCTA
AGCAGTATGTCCGTGTAATTTAACAGGAAGATAGTC
ATA		 This paper N/A
H3f3a G34V ssODN
CCGCAAATCCACCGGTGGTAAAGCACCCAGGAAAC
AACTGGCTACAAAAGCCGCTCGCAAGAGTGCGCCC
TCTACTGGAGTGGTGAAGAAACCTCACCGCTATAG
GTATTTCTAAAACGTCGAGCAGTGGGATAGTGTCTA
AGCAGTATGTCCGTGTAATTTAACAGGAAGATAGTC
ATA		 This paper N/A
H3f3a G34W ssODN
CCGCAAATCCACCGGTGGTAAAGCACCCAGGAAAC
AACTGGCTACAAAAGCCGCTCGCAAGAGTGCGCCC
TCTACTGGATGGGTGAAGAAACCTCACCGCTATAG
GTATTTCTAAAACGTCGAGCAGTGGGATAGTGTCTA
AGCAGTATGTCCGTGTAATTTAACAGGAAGATAGTC
ATA		 This paper N/A
H3f3a DKI Sanger genotyping primers:
Fwd: CGATAGATGTAATCCGCGCC
Rvs: ATCCCACTGCTCGACGTT		 This paper N/A
H3f3a inducible G34R genotyping primers:
5’ Fwd: CGCGAGCCTCTTAACTGC
5’ Rvs: GTTTACGTCGCCGTCCAG
3’ Fwd: GAGAAGCGCGATCACATGGT
3’ Rvs: TGTGTTTGTGGCTTCGTTCATT		 This paper N/A
Recombinant DNA
Software and Algorithms
Trimmomatic v0.32 Bolger et al., 2014 http://www.usadellab.org/cms/?page=trimmomatic
STAR v2.3.0e Dobin et al., 2013 https://github.com/alexdobin/STAR
featureCounts v1.4.4 Liao et al., 2014 http://bioinf.wehi.edu.au/featureCounts/
DESeq2 v1.14.1 Love et al., 2014 https://bioconductor.org/packages/release/bioc/html/DESeq2.html
fgsea v1.8.0 - https://bioconductor.org/packages/release/bioc/html/fgsea.html
BWA-MEM Li and Durbin et al., 2009 http://bio-bwa.sourceforge.net/bwa.shtml
Picard Broad Institute https://broadinstitute.github.io/picard/
IGV Robinson et al., 2011 http://software.broadinstitute.org/software/igv/
GenPipes v3.1.2 Bourgey et al., 2019 https://bitbucket.org/mugqic/genpipes/src/master/
Homer v4.9.1 Heinz et al. 2010 http://homer.ucsd.edu/homer/
VisRSeq v0.9.40 Younesy et al., 2015 https://visrsoftware.github.io/
SeqMonk BabrahamBioinformatics https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/
MACS Zhang et al., 2008 https://github.com/macs3-project/MACS
Other