NCBI Gene Manifestation Omnibus. B, Butz S, Bonora G, Sabri S, Ernst Rabbit polyclonal to ZCCHC7 J, Plath K. 2017. Cooperative binding of Oct4, Sox2, and Klf4 with stage-specific transcription factors orchestrates reprogramming. NCBI Gene Manifestation Omnibus. GSE90895Cao K, Collings CK, Shilatifard A. 2018. An Mll4/COMPASS-Lsd1 epigenetic axis governs enhancer function and pluripotency transition in embryonic stem cells. NCBI Gene Manifestation Omnibus. GSE99022Rickels RA, Collings CK, Shilatifard A. 2017. Histone H3K4 monomethylation catalyzed by Trr and mammalian COMPASS-like proteins at enhancers is definitely dispensable for development and viability. NCBI Gene Manifestation Omnibus. GSE95781Kumar V, Masafumi M, Prabhakar S. 2016. Histone acetylation H2BK20ac marks cell-state specific active regulatory elements. NCBI Gene Manifestation Omnibus. GSE72886Ishiuchi T, Sato T, Ohishi H. 2019. Zfp281 designs the transcriptome of trophoblast stem cells and is essential for placental development. NCBI Gene Manifestation Omnibus. GSE111824Adachi K, Nikaido I, Ura H, Ueda HR, Niwa H. 2014. ChIP-seq anlysis of Sox2, Tfap2c, and Cdx2 in trophoblast stem cells. NCBI Gene Manifestation Omnibus. GSE51511Liu Z, Kraus WL. 2017. Genome-wide maps of histone marks, Sox2, Oct4 and PARP-1 in mES cells. NCBI BIO-1211 Gene Manifestation Omnibus. GSE74112Suter DM. 2016. Genome-wide analysis of SOX2 binding in asynchronous and mitotic mouse embryonic stem cells. NCBI Gene Manifestation Omnibus. GSE89599Laue ED. 2017. 3D constructions of individual mammalian genomes reveal principles of nuclear business. NCBI Gene Manifestation Omnibus. GSE80280Lim B, Tam W, Orlov YL. 2009. Genome-wide maps of Tbx3 binding sites in mouse ESCs. NCBI Gene Manifestation Omnibus. GSE19219Kim J, Beck S. 2014. CpG island-mediated global gene regulatory modes in mouse embryonic stem cells. NCBI Gene Manifestation Omnibus. GSE48666Sejr Hansen A, Cattoglio C, Pustova I, Tjian R, Darzacq X. 2017. CTCF and cohesin regulate chromatin loop stability with unique dynamics. NCBI Gene Manifestation Omnibus. GSE90994Suter DM, Friman ET. 2019. Endogenous fluctuations of OCT4 and SOX2 bias pluripotent cell fate decisions. NCBI Gene Manifestation Omnibus. GSE126554Supplementary MaterialsFigure 4source data 1: Time-lapse microscopy resource data of mCherry-OCT4-AID transmission after IAA treatment (Number 4B) and washout (Number 4C). Time is in hours; Signal is the background-subtracted mean intensity; Cell is the cell unique identifier of each tracked cell; Treatment shows IAA or Washout just prior to imaging. elife-50087-fig4-data1.xlsx (104K) GUID:?E872FA3B-7FB6-4C18-BE8E-62D8155F6DAE Supplementary file 1: Additional?statistics. This file contains p-values and collapse change values for those relevant comparisons in Number 1DCG, Number 2B,C,J,K, Number 2figure product 1A,C,D,F,H, Number 2figure product 2BCG, Number 3F, Number 3figure product 2C, Number 3figure product 3D, Number 3figure product 4DCE, Number 4DCE, and Number 5figure product 1F-G. elife-50087-supp1.xlsx (48K) GUID:?7427EB82-D133-418A-BB48-6037F52D662E Supplementary file 2: Motif?analysis. This file contains enrichment ideals (logP) and frequencies of known motifs from HOMER in the following groups of loci: OD, CD, SD, OCT4 BIO-1211 OFF upregulated (OCT4up), SOX2 OFF upregulated (SOX2up), and clusters 1C4.?Only motifs with -logP < 50 in at least one group are shown. elife-50087-supp2.xlsx (75K) GUID:?D43A093B-A1D8-4E18-9DE6-944F3493F873 Supplementary file 3: Random forest magic size results. This file contains the top 500 features of the random forest model used to forecast the cluster of areas based on overlap with ChIP-seq peaks from cistromeDB annotated as belonging to mouse Sera cells.Importance ideals are derived from the model. Sample name, BIO-1211 Element, Cell collection, and GSMID refer to sample data in GEO and ID refers to the sample ID in cistromeDB. Cluster 1C4 columns show fraction of areas overlapping the sample peaks. elife-50087-supp3.xlsx (88K) GUID:?F7779867-E0E6-4436-BFDB-8329E2F7C8F4 Supplementary file 4: Primers utilized for RT-qPCR. This file contains the oligonucleotide sequences used to perform RT-qPCR experiments. elife-50087-supp4.xlsx (48K) GUID:?2D0EF892-09A6-45D9-8557-B55285BD6C2F Supplementary file 5: Published?datasets?used. This file contains descriptions of publicly available raw data that were aligned and processed according to the Materials and methods section as well as publicly available pre-processed data used in the study. elife-50087-supp5.xlsx (40K) GUID:?EAB7CAA7-54AC-4EE5-AEBB-891F553E6E78 Transparent reporting form. elife-50087-transrepform.docx (246K) GUID:?021234D5-4D54-44A1-B788-2905A5DD5F85 Data Availability StatementSequencing data have been deposited in GEO under accession BIO-1211 code “type”:”entrez-geo”,”attrs”:”text”:”GSE134680″,”term_id”:”134680″GSE134680. Resource data have been offered for Numbers 4B-C. The following dataset was generated: Friman ET, Suter DM. 2019. Dynamic rules of chromatin convenience by pluripotency transcription factors across the cell cycle. NCBI Gene Manifestation Omnibus. GSE134680 The following previously published datasets were used: King HW, Klose RJ. 2017. The pioneer element OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells. NCBI Gene Manifestation Omnibus. GSE87822 Savatier P, Aksoy I. 2014. Genome-wide mapping of Klf4 and Klf5 in pluripotent mouse embryonic stem cells (ESCs) NCBI Gene Manifestation Omnibus. GSE49848 Xiong J, Zhang Z, Chen J, Xu Y, Ding X, Nishinakamura R, Xu G, Chen S, Gao S, Zhu B. 2016. Cooperative Action Between SALL4A and TET Proteins in Stepwise.
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