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. Author manuscript; available in PMC: 2024 Aug 22.
Published in final edited form as: Cell Rep. 2023 Jan 20;42(1):112012. doi: 10.1016/j.celrep.2023.112012

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Anti-TRIM28 Cell Signaling Technology Cat #4123;
RRID:AB_2256670
Anti-Ki67 Thermo Fisher Scientific Clone SP6,
Cat # MA5–14520; RRID:AB_10979488
Anti-Collagen II Thermo Fisher Scientific Clone 6B3,
Cat # MA5–13026;
RRID: AB_10979392
Anti-Collagen X DSHB Clone X-AC9,
Cat # X-AC9;
RRID: AB_528175
Anti-IHH Millipore Cat # MABF23;
RRID: AB_10807445
Anti-Phospho-S6 Cell Signaling Technology Cat # 4858;
RRID: AB_916156
Anti-Phospho-Akt Cell Signaling Technology Clone D9E,
Cat # 4060;
RRID: AB_2315049
Anti-S6 Cell Signaling Technology Clone 5G10,
Cat # 2217;
RRID: AB_331355
Anti-Akt Cell Signaling Technology Cat # 4685;
RRID: AB_2225340
Anti-GAPDH Proteintech Cat # 10494–1-AP;
RRID: AB_2263076
Anti-GREM1 Abgent Cat # AP12247b;
RRID: AB_10819593
Anti-α-Tubulin Sigma-Aldrich Clone AA13,
Cat # T8203;
RRID: AB_1841230
Anti-phospho-4E-BP1 Cell Signaling Technology Clone 236B4,
Cat # 2855;
RRID: AB_560835
Anti-phospho-p70 S6 Kinase Cell Signaling Technology Clone 108D2,
Cat # 9234;
RRID: AB_2269803
Anti-phospho-smad1/5/8 Cell Signaling Technology Cat # 9 511;
RRID: AB_331671
Anti-H3K9me3 Abcam Cat # ab8898;
RRID: AB_306848
Anti-H3K27ac Active Motif Cat # 39133;
RRID: AB_2561016
Anti-CD45 Tonbo Biosciences Clone 30-F11
Cat # 35–0451
RRID: AB_2621689
Anti-TER-119 Tonbo Bioscience Clone TER-119
Cat # 20–5921
RRID: AB_2621609
Anti-Tie-2 BioLegend Clone TEK4
Cat # 124010
RRID: AB_10897106
Anti-CD51 Thermo Fisher Scientific Clone RMV-7
Cat # 12–0512-81
RRID: AB_465703
Anti-Thy-1.2 Thermo Fisher Scientific Clone 53–2.1
Cat # 25–0902–81
RRID: AB_469641
Anti-6C3 Thermo Fisher Scientific Clone 6C3
Cat # 46–5891-82
RRID: AB_2573797
Anti-CD105 BD Biosciences Clone MJ7/18
Cat # 562762
RRID: AB_2737776
Anti-CD200 BD Biosciences Clone OX-90
Cat # 565547
RRID: AB_2739289
Bacterial and virus strains
One Shot™ Stbl3™ chemically competent E. coli Thermo Fisher Scientific Cat #C737303
Chemicals, peptides, and recombinant proteins
Recombinant Human Gremlin1 protein PEPROTECH Cat # 120–42
YL294002 Millipore Sigma Cat # 440202
Rapamycin Selleckchem Cat #S1039
Critical commercial assays
VECTASTAIN® Elite® ABC-HRP Kit Vector Laboratories Cat # PK-6102
ImmPACT® DAB EqV Substrate Kit, Peroxidase (HRP) Vector Laboratories Cat # SK-4103
in-situ Cell Death Detection Kit Millipore Sigma Cat # 11684795910
RNeasy kit Qiagen Cat # 74004
SYBR Green QPCR Master Mix Applied biosystems™ Cat # 4309155
VILO cDNA synthesis kit Invitrogen Cat # 11754050
Quick-DNA Miniprep Plus kit Zymo Research Cat #D4068
TruSeq ChIP Library Preparation kit Illumina Cat # IP-202–1012
Cat # IP-202–1024
NEBNext Ultra II DNA Library Prep Kit NEB; Ipswich, MA Cat #E7645
ds DNA HS Assay kit Thermo Fisher Scientific Cat #Q32851
AMPure XP beads Beckman Coulter Cat # A63880
Dual-Luciferase Reporter assay kit Promega Cat #E1910
10x Chromium Next GEM Single Cell 3' GEM kit, v.3.1 10xGenomics Cat # PN-1000121
Deposited data
Raw and analyzed data This paper GEO: GSE202060
Experimental models: Cell lines
Human: 293T ATCC Cat # CRL-3216™
Mouse: ATDC5 Millipore Sigma Cat # 99072806
Experimental models: Organisms/strains
Mouse: Trim28f/f Jackson Laboratories Cat # 018552
Mouse: Dermo1-Cre Jackson Laboratories Cat # 008712
Mouse: Col2a1-Cre Jackson Laboratories Cat # 003554
Oligonucleotides
Actb qPCR primers Integrated DNA Technologies See Table S8 for sequences
Trim28 qPCR primers Integrated DNA Technologies See Table S8 for sequences
Grem1 qPCR primers Integrated DNA Technologies See Table S8 for sequences
Tubb3 qPCR primers Integrated DNA Technologies See Table S8 for sequences
Nes qPCR primers Integrated DNA Technologies See Table S8 for sequences
Mapt qPCR primers Integrated DNA Technologies See Table S8 for sequences
Gapdh qPCR primers Integrated DNA Technologies See Table S8 for sequences
Trim28-flox genotyping primer Integrated DNA Technologies See Table S8 for sequences
Cre genotyping primer Integrated DNA Technologies See Table S8 for sequences
Recombinant DNA
Lenti-CRISPRv2-puro Sanjana et al.58 Cat# 52961
RRID: Addgene_52961
Lenti-CRISPRv2-blast This paper N/A
Lenti-CRISPRv2_sgGFP This paper N/A
Lenti-CRISPRv2_sgDMR1 This paper N/A
Lenti-CRISPRv2_sgDMR2–1 This paper N/A
Lenti-CRISPRv2_sgDMR2–2 This paper N/A
pGL3-Basic vector Promega Catalog #E1751
pGL3_Grem1_Promter This paper N/A
pGL3_Grem1_Promter_DMR1 This paper N/A
pGL3_Grem1_Promter_DMR2 This paper N/A
pMD2.G pMD2.G was a gift from Didier Trono (http://n2t.net/addgene:12259) Cat# 12259
RRID: Addgene_12259
psPAX2 psPAX2 was a gift from Didier Trono (Addgene plasmid # 12260; http://n2t.net/addgene:12260) Cat# 12260
RRID: Addgene_12260
PLKO.1 puro Stewart et al.59 Cat# 8453
RRID: Addgene_8453
PLKO.1 puro_shct This paper N/A
PLKO.1 puro_shGrem1 This paper N/A
Software and algorithms
ImageJ software GraphPad https://www.graphpad.com/
NeuronJ Biomedical Imaging Group Rotterdam of Erasmus University Medical Center https://imagescience.org/meijering/software/neuronj/
FlowJo™ v10 BD Biosciences https://www.bdbiosciences.com/en-us/products/software/flowjo-v10-software
R version 4.1.0 R Foundation for Statistical Computing https://www.R-project.org