Journal: Cell reports

Article Title: Activator of KAT3 histone acetyltransferase family ameliorates a neurodevelopmental disorder phenotype in the syntaxin 1A ablated mouse model.

doi: 10.1016/j.celrep.2024.114101

Figure Lengend Snippet: Figure 3. KAT3B associates to stx1a CPR in cell/tissue expressing stx1a (A and B) ChIP assays using KAT3 antibody in PC12 (A) or FRSK (B) cells treated with TSA (+) or untreated (). Primers for the stx1a CPR were used to amplify isolated DNA. The data shown are representative images. Values indicate means (n = 3 wells; two-tailed unpaired t test) from three independent experiments.KAT3 binds to the CPR in PC12 cells, which express stx1a, but not in FRSK cells, which do not. **p < 0.01 compared to the untreated control. The KAT3B association to theCPRisledbyTSAtreatmentinFRSKcellsnotendogenouslyexpressingstx1a. (C and D) ChIP assays using KAT3 antibody in tissues of brain (C) or lung (D). Primers for the stx1a CPR were used to amplify isolated DNA. The data shown are representative images. Values indicate means (n = 3 wells; two-tailed unpaired t test) from three independent experiments. The KAT3B associates with the CPR in the brain tissue endogenously expressing stx1a, but not in the lung tissue not expressing stx1a. *p < 0.05 compared to the untreated control.

Article Snippet: Cg-Stx1a knockout mice This paper RBRC Acc# RBRC10236 Mouse: C57BL/6J, male, 2–3 months old Inbred (JNCASR) N/A Mouse: C57BL/6J The Jacksons Laboratory RRID:IMSR_JAX:008890 Oligonucleotides Oligonucleotides for EMSA and competition assays (See method details) This paper Table S3 Primers for ChIP assay (See method details) This paper Table S4 Recombinant DNA P300 short hairpin RNA plasmid Santa Cruz Biotechnology Cat# sc-29431-SH Negative control short hairpin RNA plasmid Santa Cruz Biotechnology Cat# sc-108060 pGL3-TK Promega Cat# E1751 phRG-TK Promega Cat# E6291 Software and algorithms Proteome Discoverer 1.4 Thermo Fisher Scientific https://tools.thermofisher.com/ content/sfs/manuals/ManXCALI-97506-Proteome-Discoverer14-User-ManXCALI97506-A-EN.pdf Multi Gauge 3 FujiFilm https://www.fujifilm.com/us/en Powerchrom ES280 eDAQ https://www.edaq.com/ES280 EZR1.61 Kanda Y https://www.nature.com/articles/ bmt2012244.pdf GraphPad Prism 4.03 GraphPad https://www.graphpad.com/features Other Cryotome CM3050S Leica Model# CM3050S Field Emission Scanning Electron Microscope (FESEM) Thermo Fischer (FEI) Model# APREO 2 S (Continued on next page) 14 Cell Reports 43, 114101, April 23, 2024

Techniques: Expressing, Isolation, Two Tailed Test, Control

Journal: Cell reports

Article Title: Netrin-1 feedforward mechanism promotes pancreatic cancer liver metastasis via hepatic stellate cell activation, retinoid, and ELF3 signaling.

doi: 10.1016/j.celrep.2023.113369

Figure Lengend Snippet: Figure 4. Elf3 increases expression of Netrin-1 in human and mouse pancreatic cancer cells (A) ATAC-seq analysis of the Elf3 promoter for metastatic Met38 and primary Ink4a.1 pancreatic cancer cells, n = 2/group. (B) Expression of Elf3 was determined by qPCR in multiple primary and metastatic mouse (left) and human (right) pancreatic cancer cell lines treated with 10 mM all-trans-retinoic acid (ATRA) for 18 h. Actin expression was used for normalization. In all cases except for MIAPACA-2, the increase in Elf3 mRNA was statistically significant by two-tailed t test, n = 3/group. (C) ChIP experiment to demonstrate that RARa interacts with the Elf3 promoter, n = 4/group. (D) Following 7 days of treatment with DMSO or varying concentrations of ATRA, the percentages of E-cadherin-positive (left) and vimentin-positive (right) cells were determined by flow cytometry in three cell lines, each of which had been developed from pancreatic tumors generated by different KPC-Arid1a/ mice, n = 3/group. (E) The top panel shows conservation of consensus Elf3 transcription factor binding sequence within the Netrin-1 promoter in a variety of species, while the bottom panel shows results of a ChIP experiment indicating that Elf3 interacts with this region on the mouse Ntn1 gene. (F) Ink4a.1 cells were transfected for 72 h with pCMV6 or with pCMV6-Elf3, followed by qPCR to assay Netrin-1 transcription. Actin was used as a normalization control, n = 3/group. (G) Met38 sgControl and sgElf3 were treated with DMSO or 10 mM ATRA for 18 h and analyzed for Netrin-1 RNA expression. The top graph shows the fold change of Netrin-1 expression for ATRA vs. DMSO, n = 3. All experiments were completed at least in duplicate and represent mean ± SEM. In the bottom panel the reduction of Elf3 protein is demonstrated by western blot analysis; positions of molecular weight markers, in kDa, are indicated. Statistical analysis was completed using two-tailed Student’s t test (*p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001).

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER ESE1 (ELF3) (NM_004433) Human Tagged ORF Clone Origene RC200631 Software and algorithms ImageScope software Leica Biosystems Imaging N/A VisioPharm 19 software VisioPharm N/A GraphPad Prism GraphPad N/A QuPath digital pathology analysis software https://qupath.github.io/ N/A Integrated Genome Browser https://bioviz.org/ N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ N/A Salmon https://combine-lab.github. io/salmon/getting_started/ N/A EdgeR https://bioconductor.org/ packages/release/bioc/html/ edgeR.html N/A R package GAGE https://bioconductor.org/ packages/release/bioc/html/ gage.html N/A Morpheus https://software.broadinstitute. org/morpheus/ N/A ShinyGO 0.77 http://bioinformatics.sdstate. edu/go/ N/A Other Covidien 30-gauge needles Fisher Scientific 22-557-172 CELOX Rapid Hemostatic Gauze Fisher Scientific NC1419211 Ethicon PDS II (Polydioxanone) Suture, Size 5-0, RB-1, 2700 Fisher Scientific NC1985442 BD Autoclip Wound Closing System Fisher Scientific 22–275998 Falcon Cell Culture Inserts, 8 mm Fisher Scientific 08-771-21

Techniques: Expressing, Two Tailed Test, Cytometry, Generated, Binding Assay, Sequencing, Transfection, Control, RNA Expression, Western Blot, Molecular Weight

Journal: Cell reports

Article Title: Netrin-1 feedforward mechanism promotes pancreatic cancer liver metastasis via hepatic stellate cell activation, retinoid, and ELF3 signaling.

doi: 10.1016/j.celrep.2023.113369

Figure Lengend Snippet: Figure 7. The Netrin-1 feedforward mecha- nism that promotes liver metastasis EVs containing Netrin-1 activate HSCs through both long-range (A) and possibly short-range communi- cation upon dissemination in the liver (B). Upon activation by Netrin-1, HSCs dump their retinoic acid stores (C). The free retinoic acid is taken up by DTCs by their retinoic acid receptors (D), leading to upre- gulation of Netrin-1 directly and indirectly through Elf3 upregulation. Through autocrine signaling (E) by Unc5b receptors, newly arrived DTCs increase sur- vival potential through Netrin-1 excretion. In addi- tion, activated hepatic stellate cells deposit collagen into the microenvironment (F), which over time al- lows macrometastases to become established in the liver (G).

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER ESE1 (ELF3) (NM_004433) Human Tagged ORF Clone Origene RC200631 Software and algorithms ImageScope software Leica Biosystems Imaging N/A VisioPharm 19 software VisioPharm N/A GraphPad Prism GraphPad N/A QuPath digital pathology analysis software https://qupath.github.io/ N/A Integrated Genome Browser https://bioviz.org/ N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ N/A Salmon https://combine-lab.github. io/salmon/getting_started/ N/A EdgeR https://bioconductor.org/ packages/release/bioc/html/ edgeR.html N/A R package GAGE https://bioconductor.org/ packages/release/bioc/html/ gage.html N/A Morpheus https://software.broadinstitute. org/morpheus/ N/A ShinyGO 0.77 http://bioinformatics.sdstate. edu/go/ N/A Other Covidien 30-gauge needles Fisher Scientific 22-557-172 CELOX Rapid Hemostatic Gauze Fisher Scientific NC1419211 Ethicon PDS II (Polydioxanone) Suture, Size 5-0, RB-1, 2700 Fisher Scientific NC1985442 BD Autoclip Wound Closing System Fisher Scientific 22–275998 Falcon Cell Culture Inserts, 8 mm Fisher Scientific 08-771-21

Techniques: Activation Assay

Journal: Immunity

Article Title: Age-related dopaminergic innervation augments T helper 2-type allergic inflammation in the postnatal lung

doi: 10.1016/j.immuni.2019.10.002

Figure Lengend Snippet: (A) Flow cytometry analyses of IL-2Rα (also called CD25) in Th0 cultures treated with dopamine alone and in combination with forskolin (1 μM, Fsk). Similar results were obtained in 3 independent experiments. (B) Flow cytometry analyses of CD25 and p-STAT5 in Th0+IL4 cultures of each treatment group. Similar results were obtained in 5 independent experiments. (C) Flow cytometry analyses of CD25 expression in day 2 Th0 cultures following treatment with dopamine and a STAT5 specific inhibitor, CAS285986-31-4 (20 μM). Data are representative of 3 independent experiments. (D) IL-13 production in day 2 Th0 cultures in each treatment group measured by ELISA. (E and F) The relative amount of H3K27me3 at the promoter of Il4, Il5, Il13, Il2ra and Gata3 genes in Th0 and Th0+IL-4 cultures by quantitative ChIP analyses. Bar graphs (D-F) represent mean ± SEM of three independent experiments. *p<0.05; **p<0.01 by two-tailed student’s t test. See also Figure S3.

Article Snippet: ELISA set eBioscience Cat#88-7137-76 Norepinephrine ELISA Kit Abnova Cat#89-028-610 Dopamine ELISA kit Abnova Cat#89-028-620 cAMP XP® Assay Kit Cell signaling Cat#4339S Mouse OVA Specific IgE ELISA Kit BioLegend Cat#439807 CFSE Cell Division Tracker Kit BioLegend Cat#423801 RNeasy kit Qiagen Cat#74106 Superscript III Reverse Transcriptase Kit Thermo Fisher Cat#18080-044 PicoPure RNA isolation kit Thermo Fisher Cat#KIT0204 SuperScript IV VILO Master Mix Thermo Fisher Cat#11756050 SuperSignalTM West Pico PLUS Chemiluminescent Substrate Thermo Fisher Cat#34577 Deposited Data Raw and analyzed data This paper GSE137968 Full genome sequences for Mus musculus (UCSC version mm10) UCSC https://genome.ucsc.edu/cgi-bin/hgGateway?db=mm10 Experimental Models: Organisms/Strains Mouse: Drd4 −/− : B6.129P2-Drd4/J The Jackson Laboratory JAX:008084 Mouse: OT-II: B6.Cg-Tg(TcraTcrb)425Cbn/J The Jackson Laboratory JAX:004194 Oligonucleotides Primers for ChIP PCR and qPCR ( Dettman et al., 2011 ; Tumes et al., 2013 ) See the listed, previous publications for detail Software and Algorithms FlowJo Software (version 10.5.3) FlowJo https://www.flowjo.com/ GraphPad Prism 6 GraphPad Software https://www.graphpad.com ImageJ 1.49v ImageJ https://imagej.nih.gov R (version 3.2.5) The R Foundation https://www.r-project.org/ FastQC v.0.11.2 Babraham Institute https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ TopHat (version 2.0.13) Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml HTSeq v.0.6 ( Anders et al., 2015 ) https://htseq.readthedocs.io Open in a separate window KEY RESOURCES TABLE

Techniques: Flow Cytometry, Expressing, Enzyme-linked Immunosorbent Assay, Two Tailed Test

Journal: Immunity

Article Title: Age-related dopaminergic innervation augments T helper 2-type allergic inflammation in the postnatal lung

doi: 10.1016/j.immuni.2019.10.002

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ELISA set eBioscience Cat#88-7137-76 Norepinephrine ELISA Kit Abnova Cat#89-028-610 Dopamine ELISA kit Abnova Cat#89-028-620 cAMP XP® Assay Kit Cell signaling Cat#4339S Mouse OVA Specific IgE ELISA Kit BioLegend Cat#439807 CFSE Cell Division Tracker Kit BioLegend Cat#423801 RNeasy kit Qiagen Cat#74106 Superscript III Reverse Transcriptase Kit Thermo Fisher Cat#18080-044 PicoPure RNA isolation kit Thermo Fisher Cat#KIT0204 SuperScript IV VILO Master Mix Thermo Fisher Cat#11756050 SuperSignalTM West Pico PLUS Chemiluminescent Substrate Thermo Fisher Cat#34577 Deposited Data Raw and analyzed data This paper GSE137968 Full genome sequences for Mus musculus (UCSC version mm10) UCSC https://genome.ucsc.edu/cgi-bin/hgGateway?db=mm10 Experimental Models: Organisms/Strains Mouse: Drd4 −/− : B6.129P2-Drd4/J The Jackson Laboratory JAX:008084 Mouse: OT-II: B6.Cg-Tg(TcraTcrb)425Cbn/J The Jackson Laboratory JAX:004194 Oligonucleotides Primers for ChIP PCR and qPCR ( Dettman et al., 2011 ; Tumes et al., 2013 ) See the listed, previous publications for detail Software and Algorithms FlowJo Software (version 10.5.3) FlowJo https://www.flowjo.com/ GraphPad Prism 6 GraphPad Software https://www.graphpad.com ImageJ 1.49v ImageJ https://imagej.nih.gov R (version 3.2.5) The R Foundation https://www.r-project.org/ FastQC v.0.11.2 Babraham Institute https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ TopHat (version 2.0.13) Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml HTSeq v.0.6 ( Anders et al., 2015 ) https://htseq.readthedocs.io Open in a separate window KEY RESOURCES TABLE

Techniques: Recombinant, Red Blood Cell Lysis, Cell Stimulation, Isolation, Plasmid Preparation, Staining, Enzyme-linked Immunosorbent Assay, Epinephrine ELISA, Catecholamine ELISA, Reverse Transcription, Real-time Polymerase Chain Reaction, Software

Journal: Immunity

Article Title: Age-related dopaminergic innervation augments T helper 2-type allergic inflammation in the postnatal lung

doi: 10.1016/j.immuni.2019.10.002

Figure Lengend Snippet: (A) Flow cytometry analyses of IL-2Rα (also called CD25) in Th0 cultures treated with dopamine alone and in combination with forskolin (1 μM, Fsk). Similar results were obtained in 3 independent experiments. (B) Flow cytometry analyses of CD25 and p-STAT5 in Th0+IL4 cultures of each treatment group. Similar results were obtained in 5 independent experiments. (C) Flow cytometry analyses of CD25 expression in day 2 Th0 cultures following treatment with dopamine and a STAT5 specific inhibitor, CAS285986-31-4 (20 μM). Data are representative of 3 independent experiments. (D) IL-13 production in day 2 Th0 cultures in each treatment group measured by ELISA. (E and F) The relative amount of H3K27me3 at the promoter of Il4, Il5, Il13, Il2ra and Gata3 genes in Th0 and Th0+IL-4 cultures by quantitative ChIP analyses. Bar graphs (D-F) represent mean ± SEM of three independent experiments. *p<0.05; **p<0.01 by two-tailed student’s t test. See also Figure S3.

Article Snippet: ELISA set eBioscience Cat#88-7137-76 Norepinephrine ELISA Kit Abnova Cat#89-028-610 Dopamine ELISA kit Abnova Cat#89-028-620 cAMP XP® Assay Kit Cell signaling Cat#4339S Mouse OVA Specific IgE ELISA Kit BioLegend Cat#439807 CFSE Cell Division Tracker Kit BioLegend Cat#423801 RNeasy kit Qiagen Cat#74106 Superscript III Reverse Transcriptase Kit Thermo Fisher Cat#18080-044 PicoPure RNA isolation kit Thermo Fisher Cat#KIT0204 SuperScript IV VILO Master Mix Thermo Fisher Cat#11756050 SuperSignalTM West Pico PLUS Chemiluminescent Substrate Thermo Fisher Cat#34577 Deposited Data Raw and analyzed data This paper GSE137968 Full genome sequences for Mus musculus (UCSC version mm10) UCSC https://genome.ucsc.edu/cgi-bin/hgGateway?db=mm10 Experimental Models: Organisms/Strains Mouse: Drd4 −/− : B6.129P2-Drd4/J The Jackson Laboratory JAX:008084 Mouse: OT-II: B6.Cg-Tg(TcraTcrb)425Cbn/J The Jackson Laboratory JAX:004194 Oligonucleotides Primers for ChIP PCR and qPCR ( Dettman et al., 2011 ; Tumes et al., 2013 ) See the listed, previous publications for detail Software and Algorithms FlowJo Software (version 10.5.3) FlowJo https://www.flowjo.com/ GraphPad Prism 6 GraphPad Software https://www.graphpad.com ImageJ 1.49v ImageJ https://imagej.nih.gov R (version 3.2.5) The R Foundation https://www.r-project.org/ FastQC v.0.11.2 Babraham Institute https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ TopHat (version 2.0.13) Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml HTSeq v.0.6 ( Anders et al., 2015 ) https://htseq.readthedocs.io Open in a separate window KEY RESOURCES TABLE

Techniques: Flow Cytometry, Expressing, Enzyme-linked Immunosorbent Assay, Two Tailed Test

Journal: Immunity

Article Title: Age-related dopaminergic innervation augments T helper 2-type allergic inflammation in the postnatal lung

doi: 10.1016/j.immuni.2019.10.002

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ELISA set eBioscience Cat#88-7137-76 Norepinephrine ELISA Kit Abnova Cat#89-028-610 Dopamine ELISA kit Abnova Cat#89-028-620 cAMP XP® Assay Kit Cell signaling Cat#4339S Mouse OVA Specific IgE ELISA Kit BioLegend Cat#439807 CFSE Cell Division Tracker Kit BioLegend Cat#423801 RNeasy kit Qiagen Cat#74106 Superscript III Reverse Transcriptase Kit Thermo Fisher Cat#18080-044 PicoPure RNA isolation kit Thermo Fisher Cat#KIT0204 SuperScript IV VILO Master Mix Thermo Fisher Cat#11756050 SuperSignalTM West Pico PLUS Chemiluminescent Substrate Thermo Fisher Cat#34577 Deposited Data Raw and analyzed data This paper GSE137968 Full genome sequences for Mus musculus (UCSC version mm10) UCSC https://genome.ucsc.edu/cgi-bin/hgGateway?db=mm10 Experimental Models: Organisms/Strains Mouse: Drd4 −/− : B6.129P2-Drd4/J The Jackson Laboratory JAX:008084 Mouse: OT-II: B6.Cg-Tg(TcraTcrb)425Cbn/J The Jackson Laboratory JAX:004194 Oligonucleotides Primers for ChIP PCR and qPCR ( Dettman et al., 2011 ; Tumes et al., 2013 ) See the listed, previous publications for detail Software and Algorithms FlowJo Software (version 10.5.3) FlowJo https://www.flowjo.com/ GraphPad Prism 6 GraphPad Software https://www.graphpad.com ImageJ 1.49v ImageJ https://imagej.nih.gov R (version 3.2.5) The R Foundation https://www.r-project.org/ FastQC v.0.11.2 Babraham Institute https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ TopHat (version 2.0.13) Johns Hopkins University https://ccb.jhu.edu/software/tophat/index.shtml HTSeq v.0.6 ( Anders et al., 2015 ) https://htseq.readthedocs.io Open in a separate window KEY RESOURCES TABLE

Techniques: Recombinant, Red Blood Cell Lysis, Cell Stimulation, Isolation, Plasmid Preparation, Staining, Enzyme-linked Immunosorbent Assay, Epinephrine ELISA, Catecholamine ELISA, Reverse Transcription, Real-time Polymerase Chain Reaction, Software

Journal: Cell reports

Article Title: Embryogenic stem cell-derived intestinal crypt fission directs de novo crypt genesis.

doi: 10.1016/j.celrep.2022.111796

Figure Lengend Snippet: Figure 1. Characterization of Setd4-expressing intestinal cells (A) smFISH for Setd4 and Lgr5 expression in crypt (as indicated with dotted lines). Scale bar, 30 mm. (B) CD45EpCAM+CD44+ cells were sorted for sequencing using a 10X Genomics platform (n = 6 mice, age of 8 weeks). (C) Left, unsupervised clustering of scRNA-seq data from isolated crypt cells (n = 6,653 single-cell transcriptomes as classified in Figure S1D). Right, expression of Setd4 gene. (D) Cell proportions of the indicated genes that distinguish CBCs or RSCs in crypt cells. (E) Cellular composition of Setd4+ cells. (F) Left, violin plot of Mki67 expression. Middle, expression of proliferation markers (black outline) is overlaid on the t-SNE graph. Gene-expression values are shown as median of log10(CPM). Right, analysis of co-expression of Setd4+ cells with these proliferation markers with proportions shown (n = 237 Setd4+ cells). (G) Illustration of lineage tracing strategy in Setd4cre-ERT2/+; Rosa26lsl-tdTomato mice. (H) Detection of tdTomato and Setd4 mRNA transcripts (white transition point outline) by smFISH. Scale bar, 30 mm. (I) Left, image showing examples of tdT+ cells produced at +4 positions relative to the crypt base, with dotted lines indicating crypt boundaries. Right, position of tdT+ cells at 1 dpt (n = 371 cells from five mice). Scale bar, 30 mm. (J) Schematic of a 3D confocal imaging strategy of crypt and villus. Representative z stack images of villus and crypt, with sections at different depth of z axis. Scale bar, 50 mm.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Glycerol Sangon Biotech Cat# A600232-0500 ProLongTM glass antifade mountant Thermo Fisher Cat# P36980 Isoflurane RWD Cat# R510-22 Critical commercial assays Click-iT EdU Alexa Fluor 647 Imaging Kit Thermo Fisher Cat# C10640 Advanced Cell Diagnostics RNAscope 2.0 HD Detection Kit Advanced Cell Diagnostics Cat# 323100 Deposited data Raw RNA-seq data This manuscript SRA: PRJNA741073 Experimental models: Organisms/strains Mouse: C57BL/6J Shanghai Model Organisms Center N/A Mouse: Rosa26lsl-tdTomato Jackson Laboratory JAX No. 007905 Mouse: Rosa26mT/mG Jackson Laboratory JAX No. 007676 Mouse: Setd4cre/+ Shanghai Model Organisms Center This manuscript Mouse: Setd4cre-ERT2/+ Shanghai Model Organisms Center This manuscript Oligonucleotides Primers for Setd4, see Table S1 This manuscript N/A Primers for mT/mG, see Table S1 This manuscript N/A Primers for Foxg1, see Table S1 This manuscript N/A Primers for Globin, see Table S1 This manuscript N/A Primers for tdTomato, see Table S1 This manuscript N/A Mm-Lgr5 probe Advanced Cell Diagnostics Cat# 312171-C2 Mm-Clu probe Advanced Cell Diagnostics Cat# 427891-C3 TdTomato probe Advanced Cell Diagnostics Cat# 317041-C2 Mm-Setd4 probe Advanced Cell Diagnostics Cat# 874641-C1 Bacterial dapB probe Advanced Cell Diagnostics Cat# 320871 Software and algorithms FlowJo (V10) Treestar https://www.flowjo.com/solutions/ flowjo/downloads CytExpert software (V2.3) Beckman https://www.beckman.com/flow-cytometry/ research-flow-cytometers/cytoflex/software CellRanger (V3.1.0) 10X Genomics https://support.10xgenomics.com/single- cell-gene-expression/software/pipelines/ latest/installation Seurat (V3.1.0) Satija Lab http://seurat.r-forge.r-project.org/ ZEN Blue (V2.6) Zeiss N/A Olympus FV31-SW software (V2.3) Olympus N/A Leica Application Suite X (V3.3.0.16799) Leica N/A GraphPad Prism (V8.0.1) GraphPad https://www.graphpad.com/scientificsoftware/ prism/ ImageJ (V1.52p).

Techniques: Expressing, Sequencing, Isolation, Gene Expression, Produced, Imaging

Journal: Cell reports

Article Title: Embryogenic stem cell-derived intestinal crypt fission directs de novo crypt genesis.

doi: 10.1016/j.celrep.2022.111796

Figure Lengend Snippet: Figure 3. Setd4+ cells are resistant to irradiation and produce Sca-1+ cells for tissue repair (A) Experimental overview. Setd4cre-ERT2/+; Rosa26lsl-tdTomato mice (age of 8–12 weeks) were pulsed with a single TAM injection, followed by irradiation and tissue analyses (at least three mice for each time point). (B and C) Whole-mount imaging (B) and section imaging (C) of gut tube from non-irradiated (non-IR) or irradiated (IR) mice at 1 day post irradiation (1 dpi) showing the resistance of Setd4+ cells to X-ray. Boxed areas were magnified on the right with dotted lines indicating the crypt boundaries. Scale bar, 100 mm. (D) Absolute numbers of tdT+ cells per ten crypts at 1 dpi was quantified (n = 3 mice each; two-tailed unpaired Student’s t test; data are mean ± SEM). (E) Left, detection of Olfm4 in sections of the small intestine from non-IR or IR mice at 1 dpi. Scale bar, 100 mm. Right, western blot analysis of Olfm4 in non-IR and IR groups (n = 4 mice analyzed for each; two-tailed unpaired Student’s t test; data are mean ± SEM). (F) Left, detection of tdTomato and EdU in sections from non-IR mice or IR mice with 1-h EdU incorporation at 3 dpi. Each crypt (circled with dotted lines) is magnified to the right. Right, the percentage of tdTomato+EdU+ cells was quantified (n = 3 mice analyzed for each; two-tailed unpaired Student’s t test; data are mean ± SEM). Scale bar, 50 mm. (G) Detection of tdTomato and Sca-1 with dotted lines indicating crypt boundaries. Scale bar, 50 mm. (H) Flow cytometry of Sca-1 and tdTomato in crypt cells (gating strategy plots in Figure S3B; n = 3 mice at non-IR group and n = 7 mice at IR group analyzed; two- tailed unpaired Student’s t test; data are mean ± SEM).

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Glycerol Sangon Biotech Cat# A600232-0500 ProLongTM glass antifade mountant Thermo Fisher Cat# P36980 Isoflurane RWD Cat# R510-22 Critical commercial assays Click-iT EdU Alexa Fluor 647 Imaging Kit Thermo Fisher Cat# C10640 Advanced Cell Diagnostics RNAscope 2.0 HD Detection Kit Advanced Cell Diagnostics Cat# 323100 Deposited data Raw RNA-seq data This manuscript SRA: PRJNA741073 Experimental models: Organisms/strains Mouse: C57BL/6J Shanghai Model Organisms Center N/A Mouse: Rosa26lsl-tdTomato Jackson Laboratory JAX No. 007905 Mouse: Rosa26mT/mG Jackson Laboratory JAX No. 007676 Mouse: Setd4cre/+ Shanghai Model Organisms Center This manuscript Mouse: Setd4cre-ERT2/+ Shanghai Model Organisms Center This manuscript Oligonucleotides Primers for Setd4, see Table S1 This manuscript N/A Primers for mT/mG, see Table S1 This manuscript N/A Primers for Foxg1, see Table S1 This manuscript N/A Primers for Globin, see Table S1 This manuscript N/A Primers for tdTomato, see Table S1 This manuscript N/A Mm-Lgr5 probe Advanced Cell Diagnostics Cat# 312171-C2 Mm-Clu probe Advanced Cell Diagnostics Cat# 427891-C3 TdTomato probe Advanced Cell Diagnostics Cat# 317041-C2 Mm-Setd4 probe Advanced Cell Diagnostics Cat# 874641-C1 Bacterial dapB probe Advanced Cell Diagnostics Cat# 320871 Software and algorithms FlowJo (V10) Treestar https://www.flowjo.com/solutions/ flowjo/downloads CytExpert software (V2.3) Beckman https://www.beckman.com/flow-cytometry/ research-flow-cytometers/cytoflex/software CellRanger (V3.1.0) 10X Genomics https://support.10xgenomics.com/single- cell-gene-expression/software/pipelines/ latest/installation Seurat (V3.1.0) Satija Lab http://seurat.r-forge.r-project.org/ ZEN Blue (V2.6) Zeiss N/A Olympus FV31-SW software (V2.3) Olympus N/A Leica Application Suite X (V3.3.0.16799) Leica N/A GraphPad Prism (V8.0.1) GraphPad https://www.graphpad.com/scientificsoftware/ prism/ ImageJ (V1.52p).

Techniques: Irradiation, Injection, Imaging, Two Tailed Test, Western Blot, Flow Cytometry

Journal: Cell reports

Article Title: Embryogenic stem cell-derived intestinal crypt fission directs de novo crypt genesis.

doi: 10.1016/j.celrep.2022.111796

Figure Lengend Snippet: Figure 7. Sedt4+ cells contribute to the construction of new crypts after birth (A) Experimental overview. (B) Representative images of tdT+ clones in whole mounts of crypt. The white transition points outlined are magnified in the corresponding boxed areas (n = 4 mice each point). Scale bar, 100 mm. (C) A representative whole-mount image of the crypt fission. Sections show differing z axis depths. Yellow arrows indicate a base-to-top (from Z = 1 to Z = 55) change of crypt lumens within a crypt undergoing fission. Scale bar, 20 mm. (D) Representative images of tdT+ clones in section of intestinal crypts at P6 and P15. Dotted lines indicate crypt boundaries. Scale bar, 50 mm. (E) Top, experimental overview. Bottom, representative whole-mount images of tdT+ clones at P35 and P55. Boxed areas are magnified to the right. Yellow arrows indicate the n R 2 tdT+ crypts adjacent to each other. Scale bar, 1 mm. (F) Gross morphology of the small intestine and colon at P55 (50 dpt) showing the distribution of tdT+ clones. Scale bar, 3 mm. (G) Representative images of continuous crypts organized by tdT+ cells. Scale bar, 50 mm. (H) The percentage of continuous tdT+ crypt clones in total crypt clones labeled by tdTomato from the proximal (pro) small intestine quantified at indicated chase times (n = 3 mice respectively, two-tailed unpaired Student’s t test; data are mean ± SEM). (I) Left, model summarizing two possible fluxes of tdT+ cells based on crypt fission. Right, a representative image of ribbons with continuous tdT+ crypts. Scale bar, 50 mm. (J) Experimental overview. Setd4cre-ERT2/+; Rosa26lsl-tdTomato mice were pulsed with a single TAM injection at P25 as control and chased at P75 (50 dpt). The P5 TAM-induced group was chased at P55 (50 dpt). (K) Left, representative whole-mount images of tdT+ clones (crypt-villus). Boxed areas (left) are magnified to the right. Far right, tdTomato-infiltrate crypts identified as in the left image and the percentage of continuous tdT+ crypt clones in total crypt clones labeled by tdTomato and quantified (n = 3 mice respectively analyzed, two-tailed unpaired Student’s t test; data are mean ± SEM). Scale bar, 1 mm. (L) The number of tdT+ crypts per 1-mm2 area of the proximal (Pro) or distal (Dis) small intestinal epithelium from P5 and P25 TAM-induced groups was quantified at 50 dpt (n = 90 images as K analyzed; n = 3 mice each; two-tailed Mann-Whitney test; box edges show 25th and 75th percentile, with the central point as the median and minimum and maximum values also shown). See also Figure S6.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Glycerol Sangon Biotech Cat# A600232-0500 ProLongTM glass antifade mountant Thermo Fisher Cat# P36980 Isoflurane RWD Cat# R510-22 Critical commercial assays Click-iT EdU Alexa Fluor 647 Imaging Kit Thermo Fisher Cat# C10640 Advanced Cell Diagnostics RNAscope 2.0 HD Detection Kit Advanced Cell Diagnostics Cat# 323100 Deposited data Raw RNA-seq data This manuscript SRA: PRJNA741073 Experimental models: Organisms/strains Mouse: C57BL/6J Shanghai Model Organisms Center N/A Mouse: Rosa26lsl-tdTomato Jackson Laboratory JAX No. 007905 Mouse: Rosa26mT/mG Jackson Laboratory JAX No. 007676 Mouse: Setd4cre/+ Shanghai Model Organisms Center This manuscript Mouse: Setd4cre-ERT2/+ Shanghai Model Organisms Center This manuscript Oligonucleotides Primers for Setd4, see Table S1 This manuscript N/A Primers for mT/mG, see Table S1 This manuscript N/A Primers for Foxg1, see Table S1 This manuscript N/A Primers for Globin, see Table S1 This manuscript N/A Primers for tdTomato, see Table S1 This manuscript N/A Mm-Lgr5 probe Advanced Cell Diagnostics Cat# 312171-C2 Mm-Clu probe Advanced Cell Diagnostics Cat# 427891-C3 TdTomato probe Advanced Cell Diagnostics Cat# 317041-C2 Mm-Setd4 probe Advanced Cell Diagnostics Cat# 874641-C1 Bacterial dapB probe Advanced Cell Diagnostics Cat# 320871 Software and algorithms FlowJo (V10) Treestar https://www.flowjo.com/solutions/ flowjo/downloads CytExpert software (V2.3) Beckman https://www.beckman.com/flow-cytometry/ research-flow-cytometers/cytoflex/software CellRanger (V3.1.0) 10X Genomics https://support.10xgenomics.com/single- cell-gene-expression/software/pipelines/ latest/installation Seurat (V3.1.0) Satija Lab http://seurat.r-forge.r-project.org/ ZEN Blue (V2.6) Zeiss N/A Olympus FV31-SW software (V2.3) Olympus N/A Leica Application Suite X (V3.3.0.16799) Leica N/A GraphPad Prism (V8.0.1) GraphPad https://www.graphpad.com/scientificsoftware/ prism/ ImageJ (V1.52p).

Techniques: Clone Assay, Labeling, Two Tailed Test, Injection, Control, MANN-WHITNEY

Journal: Cell reports

Article Title: Activator of KAT3 histone acetyltransferase family ameliorates a neurodevelopmental disorder phenotype in the syntaxin 1A ablated mouse model.

doi: 10.1016/j.celrep.2024.114101

Figure Lengend Snippet: Figure 2. Identification of the KAT3B function binding to OL4 (120 to 88) region (A) DNA affinity purification for MS analyses. Proteins associating with the biotinylated OL4 DNA were affinity purified from PC12 nuclear extracts by avidin beads and separated with 5%SDS-PAGE. OL4 DNA affinity-purified protein band (AP1) is indicated with an asterisk. (B) Scheme showing a putative KAT3B (P300) motif and two identified Sp/GC motifs in the CPR and the oligonucleotide probes (OL1–8) used for supershift assay. (C) Supershift assay of the OL4-protein complex. KAT3 monoclonal antibody was incubated with PC12 nuclear extract before addition of the biotinylated OL4 probe. The DNA-protein-antibody complex supershift band (SS1) is indicated with an asterisk. The enlarged image is shown in the right rectangle. (D) Effect of KAT3B suppression on promoter activity in neuronal PC12 cells transfected with stx1a CPR (204 to +2) construct. Cells were transfected by electroporation with stx1a CPR plasmids and pcDNA3 constructs expressing rat control shRNA or KAT3B shRNA. Values indicate means (n = 18 wells; two-tailed Mann-Whitney test) from six independent experiments. **p < 0.01 compared to control shRNA. (E) Effect of KAT3B suppression on STX1A protein expression in neuronal PC12 cells. Whole-cell extracts from PC12 were immunoblotted using antibodies against STX1A, KAT3, and TUBA. (F) Effect of a KAT3 inhibitor, anacardic acid (Ana), on reporter activity in PC12 cells. The pGL-CPR (204 to +2) constructs were transfected into PC12 cells, and cells were treated with 0–50 mM Ana for 24 h. Reporter activity was measured and normalized against activity of 0 mM (0.1%) DMSO. Values indicate means (n = 9 wells; Kruskal-Wallis Dunn’s post hoc test) from three independent experiments. *p < 0.05, **p < 0.01 compared to 0 mM. (G) Effect of KAT3 inhibitor, Ana, on STX1A protein expression in neuronal PC12 cells. Whole-cell extracts from PC12 were immunoblotted using antibodies against STX1A and TUBA. (H) Effect of a KAT3 activator, TTK21, on reporter activity in PC12 cells. The pGL-CPR (204 to +2) constructs were transfected into PC12 cells, and cells were treated with 0–100 mM TTK21 for 24 h. Reporter activity was measured and normalized against activity of 0 mM (0.1% DMSO). Values indicate means (n = 9 wells; Kruskal-Wallis Dunn’s post hoc test) from three independent experiments. **p < 0.01 compared to 0 mM. (I) Effect of KAT3 activator, TTK21, on STX1A protein expression in neuronal PC12 cells. Whole-cell extracts from PC12 were immunoblotted using antibodies against STX1A and TUBA. (J) Effect of a KAT3 activator, TTK21, on [3H] 5-HT release in PC12 cells. Values indicate means (n = 7 wells; two-tailed unpaired t test) from three independent experiments. **p < 0.01 compared to 0 mM.

Article Snippet: Cg-Stx1a knockout mice This paper RBRC Acc# RBRC10236 Mouse: C57BL/6J, male, 2–3 months old Inbred (JNCASR) N/A Mouse: C57BL/6J The Jacksons Laboratory RRID:IMSR_JAX:008890 Oligonucleotides Oligonucleotides for EMSA and competition assays (See method details) This paper Table S3 Primers for ChIP assay (See method details) This paper Table S4 Recombinant DNA P300 short hairpin RNA plasmid Santa Cruz Biotechnology Cat# sc-29431-SH Negative control short hairpin RNA plasmid Santa Cruz Biotechnology Cat# sc-108060 pGL3-TK Promega Cat# E1751 phRG-TK Promega Cat# E6291 Software and algorithms Proteome Discoverer 1.4 Thermo Fisher Scientific https://tools.thermofisher.com/ content/sfs/manuals/ManXCALI-97506-Proteome-Discoverer14-User-ManXCALI97506-A-EN.pdf Multi Gauge 3 FujiFilm https://www.fujifilm.com/us/en Powerchrom ES280 eDAQ https://www.edaq.com/ES280 EZR1.61 Kanda Y https://www.nature.com/articles/ bmt2012244.pdf GraphPad Prism 4.03 GraphPad https://www.graphpad.com/features Other Cryotome CM3050S Leica Model# CM3050S Field Emission Scanning Electron Microscope (FESEM) Thermo Fischer (FEI) Model# APREO 2 S (Continued on next page) 14 Cell Reports 43, 114101, April 23, 2024

Techniques: Binding Assay, Avidin-Biotin Assay, SDS Page, Incubation, Activity Assay, Transfection, Construct, Electroporation, Expressing, Control, shRNA, Two Tailed Test, MANN-WHITNEY