Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus

. 2023 May 31;42(6):112569. doi: 10.1016/j.celrep.2023.112569

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies

Rabbit monoclonal anti-H3K27ac (D5E4)	Cell Signaling Technology	Cat#8173; RRID AB_10949503
Rabbit monoclonal anti-CTCF (D31H2)	Cell Signaling Technology	Cat#3418; RRID AB_2086791
Rabbit monoclonal anti-H3K27me3 (C36B11)	Cell Signaling Technology	Cat#9733; RRID AB_2616029
Rabbit monoclonal anti-H3K4me3 (C42D8)	Cell Signaling Technology	Cat#9751; RRID AB_2616028

Critical commercial assays

SENSE mRNA-Seq Library Prep Kit V2	Lexogen	Cat#001.96
QuantSeq 3′ mRNA-Seq Library Prep Kit FWD	Lexogen	Cat#015.96
Xfect mESC Transfection Reagent	Takara Bio	Cat#631320

Deposited data

Raw and analyzed RNA-seq data	This study	GEO: GSE223445
Raw and analyzed 3′ RNA-seq data	This study	GEO: GSE223449
Raw and analyzed scRNA-seq data	This study	GEO: GSE223452
Raw and analyzed 4C data	This study	GEO: GSE223451
Raw and analyzed ChIP-seq data	This study	GEO: GSE223447
Raw and analyzed Cut&Run data	This study	GEO: GSE223448
Analyzed data of gene expression levels in different mESC compartments	GEO record GSE99366	GEO: GSE99366
Raw data of control mESCs undergoing neural differentiation	Stryjewska et al.⁷⁸	GEO: GSE75616
Raw data of EZH2 RIP-seq	Zhao et al.⁴³	GEO: GSE17064
Raw data of EZH2 and SUZ12 RIP-seq in WT mESCs	Garland et al.⁵¹	GEO: GSE137491

Experimental models: Cell lines

M. musculus: WT1: R1 wild type	This study	N/A
M. musculus: WT2: R1, wild type	This study	N/A
M. musculus: WT3: R1, wild type	This study	N/A
M. musculus: pKO1: R1, homozygous KO of Meteor promoter	This study	N/A
M. musculus: pKO2: R1, homozygous KO of Meteor promoter	This study	N/A
M. musculus: pInv: R1, homozygous inversion of Meteor promoter	This study	N/A
M. musculus: WT4: 129-C57Bl/6, wild type	Laboratory of Marc Bühler³⁴	N/A
M. musculus: WT5: 129-C57Bl/6, wild type	Laboratory of Marc Bühler³⁴	N/A
M. musculus: WT6: 129-C57Bl/6, wild type	Laboratory of Marc Bühler³⁴	N/A
M. musculus: fKO1: 129-C57Bl/6, homozygous KO of Meteor gene	Laboratory of Marc Bühler³⁴	N/A
M. musculus: fKO2: 129-C57Bl/6, homozygous KO of Meteor gene	Laboratory of Marc Bühler³⁴	N/A
M. musculus: Rz-KD: 129-C57Bl/6, homozygous insertion of a Rz sequence into Meteor	Laboratory of Marc Bühler³⁴	N/A
M. musculus: Ctrl: R1 stably expressing dCas9	This study	N/A
M. musculus: KD1: R1 stably expressing dCas9 and gRNA for KD1	This study	N/A
M. musculus: KD2: R1 stably expressing dCas9 and gRNA for KD2	This study	N/A
M. musculus: WT7: R1, wild type	This study	N/A
M. musculus: WT8: R1, wild type	This study	N/A
M. musculus: pAS1: R1, homozygous insertion of pAS/MAZ into Meteor	This study	N/A
M. musculus: pAS2: R1, homozygous insertion of pAS/MAZ into Meteor	This study	N/A
M. musculus: WT9: R1, wild type	This study	N/A
M. musculus: WT10: R1, wild type	This study	N/A
M. musculus: pEX1: R1, homozygous insertion of a Hyg/pAS/PGKp into Meteor	This study	N/A
M. musculus: pEX2: R1, homozygous insertion of a Hyg/pAS/PGKp into Meteor	This study	N/A
M. musculus: pEX3: R1, homozygous insertion of a Hyg/pAS/PGKp into Meteor	This study	N/A

Oligonucleotides

For a list of oligonucleotides used in this study see Table S1	This study	N/A

Recombinant DNA

pCas9-GFP	Ding et al.⁷⁹	Addgene plasmid #44719
pKLV-U6gRNA	Koike-Yusa et al.⁸⁰	Addgene plasmid #50946
lenti MS2-P65-HSF1_Hygro	Konermann et al.⁸¹	Addgene plasmid #61426
CSII-U6-gRNA-CBh-3xFLAG-PA-dCas9-P2A-Puro	Deposited by the laboratory of Tohru Kimura	Addgene plasmid #83306

Software and algorithms

STAR	Dobin et al.⁸²	https://github.com/alexdobin/STAR
RSEM	Li and Dewey⁸³	https://deweylab.github.io/RSEM/
DEseq2	Love et al.⁸⁴	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
MetaCell	Baran et al.⁶⁰	https://tanaylab.github.io/metacell/
KentUtils	Kent et al.⁸⁵	https://github.com/ENCODE-DCC/kentUtils