Data CitationsTsujimura T. Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo Q, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR. 2011. Reference Epigenome: ChIP-Seq Evaluation of H3K27ac in Neural Progenitor Cells; renlab.H3K27ac.NPC.02.01. NCBI Gene Manifestation Omnibus. GSM767343Dixon JR, Jung I, Selvaraj S, Ren B. 2015. Global Reorganization of Chromatin Structures during Embronic Stem Cell Differentiation. NCBI Gene Manifestation Omnibus. GSE52457Supplementary MaterialsFigure 1source data 1: 4C-seq examine matters in the provided intervals. elife-47980-fig1-data1.xlsx (49K) GUID:?5A4BB9C7-9896-4313-B187-6F1CA48E362E Shape 2source data 1: RNA-seq read counts as well as the results from the DESeq2 analyses. elife-47980-fig2-data1.xlsx (14M) GUID:?FBAC150C-C790-4206-A0E1-EDA2482BD566 Shape 3source code 1: Resource Code Document. The R code for the PCA in Shape 3. elife-47980-fig3-code1.r (4.1K) GUID:?222CD486-E31E-4E27-9A7D-CA94571832F7 Figure 3source code 2: Rabbit polyclonal to Smad2.The protein encoded by this gene belongs to the SMAD, a family of proteins similar to the gene products of the Drosophila gene ‘mothers against decapentaplegic’ (Mad) and the C.elegans gene Sma. Source Code Document_4CMYCcount.txt. The document including the 4C-seq read matters used in Shape 3-Resource Code Document. elife-47980-fig3-code2.txt (9.6K) GUID:?C7106DB7-E9EC-4A5B-BD1D-9F67323734F4 Shape 3source code 3: Resource Code Document_4CMYCcolor.txt. The document used in Shape 3-Resource Code Document to specify the dot colours in the PCA plots. elife-47980-fig3-code3.txt (463 bytes) GUID:?D937FB0A-D06E-4D13-B124-FD5A31AC4FB0 Shape 3source code 4: Source Code Document_4CMYCshape.txt. The document used in Shape 3-Resource Code Document to specify the dot styles in the PCA plots. elife-47980-fig3-code4.txt (344 bytes) GUID:?85207D22-1FA3-424A-8E38-30D6B94B0E61 Shape 3source data 1: 4C-seq read matters in the given intervals. elife-47980-fig3-data1.xlsx (52K) GUID:?1BA5E231-485E-44D9-9027-59D221D7D850 Figure 4source data 1: nChIP-seq read matters in the peaks for H3K4me3, H3K27me3, and H3K27ac. elife-47980-fig4-data1.xlsx (2.1M) GUID:?AFAE8559-93CF-4D1F-8C50-73C2982D03A6 Shape 5source data 1: 4C-seq read counts in the given intervals, and CTCF nChIP-seq read counts in the peaks. elife-47980-fig5-data1.xlsx (662K) GUID:?20D1C1BF-8F9E-4D87-84C0-54A5D5616E9B Shape 6source data 1: 4C-seq read matters in the specific intervals, and the full total outcomes of nChIP-qPCR for H3K4me3 and H3K27me3. elife-47980-fig6-data1.xlsx (47K) GUID:?6EFD1DEB-15DB-42AE-B60F-33BBEF60CD5E Shape 7source data 1: expression levels upon removal of DOX with DMSO or EPZ. elife-47980-fig7-data1.xlsx (40K) GUID:?CCE0D257-8896-49F0-BD4D-5CCAE363B964 Shape 8source code 1: Resource Code Document_4CNGN2color.txt. The document used in Shape 3-Resource Code Document to specify the dot colours in the PCA plots. elife-47980-fig8-code1.txt (111 bytes) GUID:?E8008AF4-3516-4358-A843-DB54F191D03E Shape 8source code 2: Source Code Document_4CNGN2count.txt. The document including the 4C-seq read matters used in Shape 3-Resource Code Document. elife-47980-fig8-code2.txt (1.5K) Penicillin V potassium salt GUID:?5176F7F8-2BF3-4E10-BC25-EAAA29A4E88A Shape 8source code 3: Source Code Document_4CNGN2shape.txt. The file used in Figure 3-Source Code File to specify the dot shapes in the PCA plots. elife-47980-fig8-code3.txt (92 bytes) GUID:?A0D3E9E8-254C-40F4-B4F9-9B37C9E11F1A Figure 8source data 1: Relative gene expression levels of in differentiating NPCs, and 4C-seq read counts in the given intervals. elife-47980-fig8-data1.xlsx (13K) GUID:?7C2B901F-5B0E-4C49-9DA6-021417C6C162 Figure 8figure supplement 2source code Penicillin V potassium salt 1: Source Code File. The R code for the PCA in Figure 8figure supplement 2C. elife-47980-fig8-figsupp2-code1.r (3.5K) GUID:?5E28E1FF-0F60-4EE0-968D-B1513221C6FA Supplementary file 1: Tables for DNA sequences of oligo DNAs, of gRNA target sites, of the STITCH construct, and of indexes for NGS libraries. (A)?List of guide RNAs for CRISPR genome editing used in the study.?(B) The DNA sequences of the elements composing STITCH. (C) List of primers used to prepare the targeting cassettes. (D) List of primers used for the genotyping. (E) List of primers used in the qPCR assays. (F) List of primers used for the 4C Penicillin V potassium salt 1st PCR. (G) List of primers used to prepare the NGS libraries. (H) List of the NGS libraries. elife-47980-supp1.xlsx (31K) GUID:?4CC170E3-707B-47D9-912B-3F5275C610CF Transparent reporting form. elife-47980-transrepform.docx (246K) GUID:?93F692FB-7128-4C6D-A7F7-230E15027F43 Data Availability StatementAllthe deep sequencing data of the 4C-seq, RNA-seq and nChIP-seqlibraries analyzed in this study were deposited in ArrayExpress:E-MTAB-7668, E-MTAB-7669, E-MTAB-7670, E-MTAB-8492, andE-MTAB-8957. The following datasets were generated: Tsujimura T. 2019. RNA-seq of wild type (Hap), insulation (STITCH+30kb) and deletion (del(30-440)) of the MYC enhancer in human iPS cells. ArrayExpress. E-MTAB-7669 Tsujimura T. 2019..