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. Author manuscript; available in PMC: 2021 Mar 23.
Published in final edited form as: Dev Cell. 2020 Mar 23;52(6):699–713.e11. doi: 10.1016/j.devcel.2020.02.011

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Alexa-647-conjugated anti-phospho-
Ser22-LMNA antibody D2B2E		 Cell Signaling Cat # 97262BC, Lot 1
Anti-phospho-Ser22-LMNA antibody
D2B2E		 Cell Signaling Cat # 13448S, Lot 1; RRID:AB_2798221
Anti-pan-N-terminal-LMNA antibody E1 Santa Cruz
Biotechnology		 Cat # sc-376248, Lot H2812;
RRID:AB_10991536
Anti-full-length-LMNA antibody 4C4 Abcam Cat # ab190380, Lot GR201137–1;
RRID:AB_2747781
Anti-c-Jun antibody H-79 Santa Cruz
Biotechnology		 Cat # sc-1694, Lot D1014; RRID:AB_631263
Anti-H3K27ac antibody MABI0309 Wako Cat # 306–34849, MABI0309, Lot 14007;
RRID:AB_11126964
Anti-H3K4me3 antibody MABI0304 Wako Cat # 305–34819, MABI0304, Lot 14004;
RRID:AB_11123891
Anti-H3K9me3 antibody ab8898 Abcam Cat # ab8898, Lot GR232099–3;
RRID:AB_306848
Anti-H3K27me3 antibody MABI0323 Active Motif Cat # MABI0323, Lot 17019020;
RRID:AB_11123929
Anti-BrdU antibody 3D4 BD Biosciences Cat # 555627, Lot 7033666;
RRID:AB_395993
Chemicals, Peptides, and Recombinant Proteins
LMNA aa2–30 peptide:
ETPSQRRATRSGAQASSTPLSPTRITRL
Q		 GenScript GenScript U2312EI090–1/PE2183
LMNA aa2–30 peptide with phospho-S22:
ETPSQRRATRSGAQASSTPL[phospho-
S]PTRITRLQ		 GenScript GenScript U2312EI090–3/PE2186
Phosphatase inhibitor Nodularin Enzo Cat # ALX-350–061
Deposited Data
Genomic dataset IDs with sample
description		 This paper https://github.com/kohta-ikegami/pS22-LMNA/blob/master/datasets.md
Blacklisted regions used in this study This paper https://github.com/kohta-ikegami/pS22-LMNA/blob/master/blacklist.bed
pS22-Lamin A/C binding sites in BJ-5ta This paper https://github.com/kohta-ikegami/pS22-LMNA/blob/master/D2B2E_BJ5ta.narrowPeak
Lamin A/C LADs in BJ-5ta This paper https://github.com/kohta-ikegami/pS22-LMNA/blob/master/E1_BJ5ta_LAD.bed
ATAC-seq-defined accessible chromatin
sites in BJ-5ta		 This paper https://github.com/kohta-ikegami/pS22-LMNA/blob/master/ATAC_BJ5ta.narrowPeak
H3K27ac-enriched sites in BJ-5ta This paper https://github.com/kohta-ikegami/pS22-LMNA/blob/master/H3K27ac_BJ5ta.narrowPeak
H3K4me3-enriched sites in BJ-5ta This paper https://github.com/kohta-ikegami/pS22-LMNA/blob/master/H3K4me3_BJ5ta.narrowPeak
c-Jun-binding sites in BJ-5ta This paper https://github.com/kohta-ikegami/pS22-LMNA/blob/master/Jun_BJ5ta.narrowPeak
Genes linked to pS22-Lamin A/C sites
with GRO-seq coverage in BJ-5ta		 This paper https://github.com/kohta-ikegami/pS22-LMNA/blob/master/gene_pS22-LMNA.bed
Differentially-expressed genes in progeria This paper https://github.com/kohta-ikegami/pS22-LMNA/blob/master/progeria_gene.bed
Gained and lost pS22-Lamin A/C-binding
sites in progeria		 This paper https://github.com/kohta-ikegami/pS22-LMNA/blob/master/progeria_gained_lost_pS22-LMNA.bed
Gained and lost LADs in progeria This paper https://github.com/kohta-ikegami/pS22-LMNA/blob/master/progeria_gained_lost_LAD.bed
Progeria-up genes linked to gained pS22-
Lamin A/C-binding sites		 This paper https://github.com/kohta-ikegami/pS22-LMNA/blob/master/progeria-up_gene.txt
Human reference sequence used UCSC genome
browser		 hg19/GRCh37
Gene annotation Gencode/UCSC
genome browser		 Version 19;
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/wgEncodeGencodeBasicV19.txt.gz
High-throughput sequencing data This paper GEO accession number GSE113354
Hg19 assembly gaps UCSC genome
browser		 http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/gap.txt.gz
ENCODE blacklist UCSC genome
browser		 http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed.gz
Chromatin annotation NIH Roadmap
Epigenomics		 http://egg2.wustl.edu/roadmap/data/byFileType/chromhmmSegmentations/ChmmModels/coreMarks/jointModel/final/E126_15_coreMarks_stateno.bed.gz
Lamin B1 LADs Gluelen et al., 2008 http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/laminB1Lads.txt.gz
Progeria fibroblast RNA-seq datasets Fleischer et al., 2018 GEO accession number GSE113957
Experimental Models: Cell Lines
BJ-5ta fibroblast cell line ATCC Cat# CRL-4001; RRID:CVCL_6573
BJ-5ta-derived LMNA–/– cell line This paper Ikegami lab ID: cc1170–1AD2
GM07492 normal primary fibroblast Coriell Cell
Repository		 GM07492; RRID:CVCL_7467
GM08398 normal primary fibroblast Coriell Cell
Repository		 GM08398; RRID:CVCL_7481
AG11498 HGPS primary fibroblast Coriell Cell
Repository		 AG11498; RRID:CVCL_H766
HGADFN167 HGPS primary fibroblast Progeria Research
Foundation		 HGADFN167; RRID:CVCL_1Y92
Oligonucleotides
DNA oligonucleotide KI223 for sgRNA1
targeting exon1 of LMNA:
CACCGCATCGACCGTGTGCGCTCGC		 IDT Ikegami lab ID: KI223
DNA oligonucleotide KI224 for sgRNA1
targeting exon1 of LMNA:
AAACGCGAGCGCACACGGTCGATGC		 IDT Ikegami lab ID: KI224
DNA oligonucleotide KI227 for sgRNA3
targeting exon1 of LMNA:
CACCGCGGCATCAAGGCCGCCTACG		 IDT Ikegami lab ID: KI227
DNA oligonucleotide KI228 for sgRNA3
targeting exon1 of LMNA:
AAACCGTAGGCGGCCTTGATGCCGC		 IDT Ikegami lab ID: KI228
DNA oligonucleotide KI361 for S22A
Lamin A/C N-terminus:
GGGGACAAGTTTGTACAAAAAAGCAG
GCTGCCATGGCTTGTCCTAAAGATCC
AGCCAAACCTCCGGCCAAGGCACAAG
TTGTGGGATGGCCACCGGTGAGATCA
TACCGGAAGAACGTGATGGTTTCCTG
CCAAAAATCAAGCGGTGGCCCGGAGG
CGGCGGCGTTCGTGAAGGAGACCCC
GTCCCAGCGGCGCGCCACCCGCAGC
GGGGCGCAGGCCAGCTCCACTCCGC
TGGCTCCCACCCGCATCACCCGGCTG
CAGGAGAAGGAGGACCTGCAGGAGC
TCAATGATCGCTTGGCGGTCTATATTG
ATAGGGTCCGGAGTCTCGAAACGGAG
AACGCAGGGCTGCGCCTTCGCATCAC
CGAGTCTGAAGAGGTGGTCAGCCGCG
AGGTGTCTGGAATTAAAGCTGCTTATG
AAGCCGAGCTCGGGGATGCCCGCAA
GACCCTTGACTCAGTAGCCAAGGAGC
GCGCCCGCCTGCAGCTGGAGCTGAG
CAAAGTGCGT		 IDT Ikegami lab ID: KI361
DNA oligonucleotide KI362 for S22D
Lamin A/C N-terminus:
GGGGACAAGTTTGTACAAAAAAGCAG
GCTGCCATGGCTTGTCCTAAAGATCC
AGCCAAACCTCCGGCCAAGGCACAAG
TTGTGGGATGGCCACCGGTGAGATCA
TACCGGAAGAACGTGATGGTTTCCTG
CCAAAAATCAAGCGGTGGCCCGGAGG
CGGCGGCGTTCGTGAAGGAGACCCC
GTCCCAGCGGCGCGCCACCCGCAGC
GGGGCGCAGGCCAGCTCCACTCCGC
TGGACCCCACCCGCATCACCCGGCTG
CAGGAGAAGGAGGACCTGCAGGAGC
TCAATGATCGCTTGGCGGTCTATATTG
ATAGGGTCCGGAGTCTCGAAACGGAG
AACGCAGGGCTGCGCCTTCGCATCAC
CGAGTCTGAAGAGGTGGTCAGCCGCG
AGGTGTCTGGAATTAAAGCTGCTTATG
AAGCCGAGCTCGGGGATGCCCGCAA
GACCCTTGACTCAGTAGCCAAGGAGC
GCGCCCGCCTGCAGCTGGAGCTGAG
CAAAGTGCGT		 IDT Ikegami lab ID: KI362
DNA oligonucleotide KI393 for S392A
Lamin A/C C-terminal cloning:
TGGAGCTGAGCAAAGTGCGT		 IDT Ikegami lab ID: KI393
DNA oligonucleotide KI385 for S392A
Lamin A C-terminal cloning:
TCGTGGCTCCGGAACCGGTGTTACAT
GATGCTGCAGTTCT		 IDT Ikegami lab ID: KI385
DNA oligonucleotide KI395 for S392A
Lamin C C-terminal cloning:
TCGTGGCTCCGGAACCGGTGTCAGCG
GCGGCTACCACTCACGTGGTGGTGAT
GGAGCAGG		 IDT Ikegami lab ID: KI395
Recombinant DNA
LentiCRISPRv2 Sanjana et al., 2014 Addgene plasmid #52961
psPAX2 Didier Trono lab Addgene plasmid #12260
pCMV-VSV-G Stewart et al., 2003 Addgene plasmid #8454
pCW57-MCS1-P2A-MCS2-PGK-Blast Barger et al. 2019 Addgene plasmid #80921
Wild-type Lamin A cDNA in pCW57-
MCS1-P2A-MCS2-PGK-Blast		 This paper Ikegami lab ID: bKI218
Lamin A-S22A/S392A cDNA in pCW57-
MCS1-P2A-MCS2-PGK-Blast		 This paper Ikegami lab ID: bKI226
Lamin A-S22D/S392D cDNA in pCW57-
MCS1-P2A-MCS2-PGK-Blast		 This paper Ikegami lab ID: bKI241
Wild-type Lamin C cDNA in pCW57-
MCS1-P2A-MCS2-PGK-Blast		 This paper Ikegami lab ID: bKI247
Lamin C-S22A/S392A cDNA in pCW57-
MCS1-P2A-MCS2-PGK-Blast		 This paper Ikegami lab ID: bKI242
Lamin C-S22D/S392D cDNA in pCW57-
MCS1-P2A-MCS2-PGK-Blast		 This paper Ikegami lab ID: bKI245
Software and Algorithms
R The R foundation R 3.3.2
Bowtie aligner Langmead and Salzberg, 2012 Version 2.1.0
Bedtools Quinlan and Hall, 2010 Version 2.26.0
DESeq2 Love et al., 2014 Version 1.14.1
MACS2 Zhang et al., 2008 Version 2.1.0
MEME Machanick and Bailey, 2011 Version 4.10.0
R package stats The R foundation Version 3.3.2
R package preprocessCore Bolstad et al., 2003 Version 1.36.0
Metascape Tripathi et al., 2015 http://metascape.org/