| Antibodies |
| Rabbit monoclonal anti-MeCP2 (clone D4F3) |
Cell Signaling Technology |
#3456; RRID: AB_2143894 |
| Rabbit monoclonal anti-Tri-Methyl-Histone H3 (Lys27) [H3K27me3] (clone C36B11) |
Cell Signaling Technology |
#9733; RRID: AB_2616029 |
| Rabbit monoclonal anti-Acetyl-Histone H3 (Lys27) [H3K27ac] (clone D5E4) |
Cell Signaling Technology |
#8173, RRID: AB_10949503 |
| Rabbit polyclonal anti-Tri-Methyl-Histone H3 (Lys9) [H3K9me3] |
Abcam |
#ab8898; RRID: AB_306848 |
| Rabbit monoclonal anti-Acetyl-Histone H3 (Lys9) [H3K9ac] (clone C5B11) |
Cell Signaling Technology |
#9649, RRID: AB_823528 |
| Mouse monoclonal anti-Di and Tri-Methyl-Histone H3 (Lys20) [H4K20me2/3] (clone 6F8-D9) |
Abcam |
#ab78517, RRID: AB_1951279 |
| Rabbit polyclonal IgG |
Millipore |
#12–370, RRID: AB_145841 |
| Mouse monoclonal anti-Vinculin (clone hVIN-1) |
MilliporeSigma |
#V9131, RRID: AB_477629 |
| Mouse monoclonal anti-GAPDH (clone 6C5) |
Advanced ImmunoChemical Inc. |
#2-RGM2, RRID: AB_2721282 |
| Chicken polyclonal anti-alpha tubulin |
Abcam |
#ab89984, RRID: AB_10672056 |
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| Bacterial and virus strains |
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| Biological samples |
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| Chemicals, peptides, and recombinant proteins |
| Tamoxifen |
Sigma-Aldrich |
#T5648 |
| Peanut oil |
Sigma-Aldrich |
#P2144 |
| OptiPrep density gradient |
Sigma-Aldrich |
#D15556
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| Spermidine |
Sigma-Aldrich |
#S0266 |
| Ultrapure BSA |
Invitrogen |
#AM2618 |
| cOmplete protease inhibitor |
Roche |
#11873580001 |
| Digitonin |
Calbiochem |
#11024–24–1 |
| pAG-MNase |
Epicypher |
#15–1016 |
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| Critical commercial assays |
| Qiagen miRNeasy Mini |
Qiagen |
#217004 |
| Qiagen RNase free DNase |
Qiagen |
#79254 |
| NEB Next II DNA Ultra Kit |
New England Biolabs |
#E7645S |
| Unique Combinatorial Dual index kit |
New England Biolabs |
#E6440S, #E6442S, #E6444S |
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| Deposited data |
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Mecp2 Adult Knockout RNA-sequencing (raw and processed) |
This study |
GEO: GSE246119
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Mecp2 Adult Knockout CUT&RUN (raw and processed) |
This study |
GEO: GSE246664
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Mecp2-G118E RNA-sequencing (raw and processed) |
This study |
GEO: GSE277077
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Mecp2-null Cortex RNA-sequencing |
Zhou et al.36
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GEO: GSE179229
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Mecp2-null Cortex RNA-sequencing |
Clemens et al.10
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GEO: GSE123372
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Mecp2-null Cortex RNA-sequencing |
Boxer et al.9
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GEO: GSE128178
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Mecp2-R306C Cortex RNA-sequencing |
Boxer et al.9
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GEO: GSE128178
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Mecp2-null Hypothalamus RNA-sequencing |
Chen et al.20
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GEO: GSE66870
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Mecp2-null Cerebellum RNA-sequencing |
Raman et al.37
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GEO: GSE105045
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| Reduced representation bisulfite sequencing of hippocampus |
Reizel et al.41
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GEO: GSE85251
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| Hippocampal RNA-seq used in deconvolution |
Habib et al.67
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GEO: GSE143758
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| Hippocampal RNA-seq used in deconvolution |
Methi et al.68
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GEO: GSE234278
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| Experimental models: Cell lines |
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| Experimental models: Organisms/strains |
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B6.129S4(C)-Mecp2tm1Jae/Mmucd
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MMRCC |
MMRCC# 011918-UCD,; RRID:MMRRC 011918-UCD |
| B6.Cg-Ndor1Tg(UBC-cre/ERT2)1Ejb/1J
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The Jackson Labs |
Jax #007001; RRID: IMSR_JAX:007001 |
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Mecp2-G118E |
Zhou et al.36
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N/A |
| C57BL6/J |
The Jackson Labs |
Jax #000664; IMSR_JAX:000664 |
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| Oligonucleotides |
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Ppia qPCR forward primer: |
This paper |
N/A |
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Ppia qPCR reverse primer |
This paper |
N/A |
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Mecp2 qPCR forward primer: |
This paper |
N/A |
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Mecp2 qPCR reverse primer: |
This paper |
N/A |
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| Recombinant DNA |
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| Software and algorithms |
| STAR aligner |
Dobin et al.65
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https://github.com/alexdobin/STAR
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| DESeq2 |
Love et al.66
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https://bioconductor.org/packages/release/bioc/html/DESeq2.html
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| CIBERSORTx |
Newman et al.71
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https://cibersortx.stanford.edu/
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| Bismark |
Krueger and Andrews75
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https://github.com/FelixKrueger/Bismark
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| samtools |
Li et al.76
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https://www.htslib.org/
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| Trimmomatic |
Bolger et al.64
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http://www.usadellab.org/cms/?page=trimmomatic
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| Trimgalore |
N/A |
https://github.com/FelixKrueger/TrimGalore
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| bedtools |
Quinlan and Hall77
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https://bedtools.readthedocs.io/en/latest/
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| MACS2 |
Zhang et al.87
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https://pypi.org/project/MACS2/
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| edgeR |
Robinson et al.72
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https://bioconductor.org/packages/release/bioc/html/edgeR.html
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| deepTools |
Ramirez et al.79
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https://deeptools.readthedocs.io/en/develop/
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| Other |
|
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| Concavalin A magnetic beads |
Bangs Laboratories Inc. |
#BP531 |
| SPRI select beads |
Beckman Coulter |
#B23318
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| E. coli spike in |
Epicypher |
#18–1401 |
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