{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Amelia Hopkin"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-42180"],"description":["The antagonistic actions of Polycomb and Trithorax are responsible for proper cell fate determination in mammalian tissues. In the epidermis, a self-renewing epithelium, previous work has shown that release from Polycomb repression only partially explains differentiation gene activation. We now show that Trithorax is also a key regulator of epidermal differentiation, not only through activation of genes repressed by Polycomb in progenitor cells, but also through activation of genes independent of regulation by Polycomb. The differentiation associated transcription factor GRHL3/GET1 recruits the ubiquitously expressed Trithorax complex to a subset of differentiation genes. Examination of WDR5 and GRHL3 binding in human differentited primary keratinocytes (NHEK). High calcium medium was added to NHEK cells at 50% confluency to induce differentiation. Cells were collected for ChIP 24 hours after addition of high calcium medium. ChIP with Wdr5 and Grhl3 antibodies, and an input control were sequenced."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - NHEK cells were grown in DermaLife medium (LifeLine Cell Technologies) at 37C, 5%CO2","Sample Processing - Medium containing high calcium levels (1.8mM) was used to induce differentiation in NHEK cells. Cells were collected 24 hours after the switch to high calcium medium","Library Construction - Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. 24 ug of sonicated chromatin was used for each IP. The following antibodies were used : Grhl3 (Andersen Lab), WDR5 (AbCam cat#ab56919) Sequencing libraries were generated for the GRHL3, WDR5, and Input samples using the NEB Next reagents and Illumina adaptors and oligos, according to the Illumina protocol for ChIP-Seq library preparation, with some modification. After adaptor ligation, PCR amplification was performed prior to size selection of the library [PMID 19275939]. Clustering and 50-cycle single end sequencing were performed on the Illumina Hi-Seq 2000 Genome Analyzer."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Feature Extraction - Base-calls were made using RTA version 1.12.4.2. Reads were aligned to human genome hg19 using Bowtie version 0.12.7, only uniquely aligning reads were retained (-m 1) Bam file were converted to BED using Bedtools (bamToBed v2.11.2) Peaks were called using macs14, with input aligned sequences as the control file, m fold of 8,30, and p-value 1e-7 Galaxy was used for further data analysis (performing intersection/subtraction analysis, extracting features) Genome_build: Human hg19 Supplementary_files_format_and_content: interval files from galaxy, containing chromosome and coordinates of peak locations"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["The antagonistic actions of Polycomb and Trithorax are responsible for proper cell fate determination in mammalian tissues. In the epidermis, a self-renewing epithelium, previous work has shown that release from Polycomb repression only partially explains differentiation gene activation. We now show that Trithorax is also a key regulator of epidermal differentiation, not only through activation of genes repressed by Polycomb in progenitor cells, but also through activation of genes independent of regulation by Polycomb. The differentiation associated transcription factor GRHL3/GET1 recruits the ubiquitously expressed Trithorax complex to a subset of differentiation genes."],"study_type":["ChIP-seq"],"species":["Homo sapiens"],"pubmed_title":["GRHL3/GET1 and trithorax group members collaborate to activate the epidermal progenitor differentiation program."],"pubmed_authors":["Amelia Hopkin","Bogi Andersen","Hopkin AS, Gordon W, Klein RH, Espitia F, Daily K, Zeller M, Baldi P, Andersen B"],"additional_accession":[]},"is_claimable":false,"name":"Genome-wide binding of WDR5 and GRHL3","description":"The antagonistic actions of Polycomb and Trithorax are responsible for proper cell fate determination in mammalian tissues. In the epidermis, a self-renewing epithelium, previous work has shown that release from Polycomb repression only partially explains differentiation gene activation. We now show that Trithorax is also a key regulator of epidermal differentiation, not only through activation of genes repressed by Polycomb in progenitor cells, but also through activation of genes independent of regulation by Polycomb. The differentiation associated transcription factor GRHL3/GET1 recruits the ubiquitously expressed Trithorax complex to a subset of differentiation genes. Examination of WDR5 and GRHL3 binding in human differentited primary keratinocytes (NHEK). High calcium medium was added to NHEK cells at 50% confluency to induce differentiation. Cells were collected for ChIP 24 hours after addition of high calcium medium. ChIP with Wdr5 and Grhl3 antibodies, and an input control were sequenced.","dates":{"release":"2012-11-10T00:00:00Z","modification":"2023-08-29T18:12:39.496Z","creation":"2022-02-03T01:21:03.56Z"},"accession":"E-GEOD-42180","cross_references":{"pubmed":["22829784"],"ENA":["SRP017136"],"EFO":["EFO_0002692"],"doi":["10.1371/journal.pgen.1002829"]}}