REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Antibodies | ||
polyclonal rabbit anti-m6A (and m6Am) | Synaptic Systems | 202 003; RRID: AB_2279214 |
polyclonal rabbit anti-METTL3 | Proteintech | 15073-1-AP; RRID: AB_2142033 |
monoclonal mouse anti-FTO | Merck Millipore | MABE227; RRID: AB_11203491 |
polyclonal rabbit anti-ACTB | Cell Signaling Technology | 4967; RRID: AB_330288 |
monoclonal rabbit anti-GR | Abcam | ab109022; RRID: AB_10863164 |
polyclonal rabbit anti-BTUB | Abcam | ab6046; RRID: AB_2210370 |
Chemicals, Peptides, and Recombinant Proteins | ||
corticosterone-HBC complex | Sigma | C174 |
Dexa-ratiopharm | Ratiopharm | Dexa-ratiopharm Injektionslösung 59988.00.00 |
cycloheximide | Sigma | C7698 |
Critical Commercial Assays | ||
EpiQuik m6A RNA Methylation Quantification Kit (Colorimetric) | Epigentek | P-9005-96 |
TruSeq Stranded mRNA Library Prep Kit | Illumina | RS-122-2103 |
TruSeq Ribo Profile for Mammalian | Illumina | RPHMR12126 |
QuantiFast SYBR Green PCR Kit | QIAGEN | 204057 |
TaqMan Fast Advanced Master Mix | Applied Biosystem | 4444965 |
Deposited Data | ||
superseries | This paper | GEO: GSE113801 |
m6A/m-Seq mouse cortex after acute stress | This paper | GEO: GSE113781 |
Ribosome profiling Seq mouse cortex after acute stress | This paper | GEO: GSE113789 |
m6A/m-Seq of mouse adult cortex of Mettl3 cKO or Fto cKO mice | This paper | GEO: GSE113793 |
mRNA-Seq of mouse Mettl3 cKO or Fto cKO mouse hippocampus after fear conditioning | This paper | GEO: GSE113796 |
m6A/m-Seq of human B-lymphocyte cell lines from healthy controls and major depressive disorder patients | This paper | GEO: GSE113798 |
FMR1 bound genes | Darnell et al., 2011 | Darnell et al., 2011 Supplemental Data |
Experimental Models: Cell Lines | ||
Human immortalized BLCLs from patients | This paper | N/A |
Experimental Models: Organisms/Strains | ||
10-12 w old adult male mice C57BL/6 | Charles River | 027 |
Mettl3 cKO mice | Mettl3tm1a(KOMP)Wtsi V6.5 mouse ESCs targeted as described in mice generated by Geula et al., 2015 | Mettl3tm1c(KOMP)Wtsi |
Fto cKO mice | Ftotm1a(EUCOMM)Wtsi EMMA EM: 05094 | Ftotm1c(EUCOMM)Wtsi |
Camk2a-Cre mice | Minichiello et al., 1999 | Tg(Camk2a-cre)93Kln MGI:2176754 |
Nex-CreERT2 mice | Agarwal et al., 2012 | Neurod6tm2.1(cre/ERT2)Kan MGI:5308766 |
Human blood | Menke et al., 2012, Arloth et al., 2015 | “MPIP” and “MARS” cohorts |
Oligonucleotides | ||
Gene expression primers for SYBR green qPCR: sequences see Gene expression | Sigma-Aldrich | N/A |
Taqman gene expression assays: IDs see Candidate m6A/m-RIP-qPCR | Taqman | N/A |
m6A-spike-in-oligo GCAGAACCUAGUAG CGUGUGGm6ACACGAACAGGUAUCAAU AUGCGGGUAUGGm6ACUAAAGCAACGUG CGAGAUUACGCUGAGGm6ACUACAAUCU 'CAGUUACCA |
Sigma-Aldrich | N/A |
primers for cloning ISH probes: Mettl3 exon 4 TCAGTCAGGAGATCCTAGAGCTATT and CTGAAGTGCAGCTTGCGACA; Fto exon 4 TGGCAGCTGAAATACCCTAAACT and ATAG CTGTACACTGCCACGG) |
Sigma-Aldrich | N/A |
Software and Algorithms | ||
STAR | Dobin et al., 2013 | RRID: SCR_015899 |
cutadapt | Martin, 2011 | RRID: SCR_011841 |
exomePeak | Meng et al., 2014 | RRID: SCR_001076 |
BEDTools | Quinlan and Hall, 2010 | RRID: SCR_006646 |
DiffBind | Ross-Innes et al., 2012 | RRID: SCR_012918 |
DESeq2 | Love et al., 2014 | RRID: SCR_015687 |
ChIPseeker | Yu et al., 2015 | https://doi.org/10.18129/B9.bioc.ChIPseeker |
BioMart Project | Smedley et al., 2015 | RRID: SCR_002987 |
Guitar | Cui et al., 2016 | https://doi.org/10.18129/B9.bioc.Guitar |
PANTHER GO | Mi et al., 2013 | RRID: SCR_004869 |
DREME | Bailey, 2011 | RRID: SCR_001783 |
Integrative Genomics Viewer browser | Robinson et al., 2011 | RRID: SCR_011793 |
SPSS | IBM SPSS Statistics | RRID: SCR_002865 |
R | R Development Core Team, 2011 | RRID: SCR_001905 |
ggplot2 | Wickham, 2009 | RRID: SCR_014601 |