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Series GSE200808 Query DataSets for GSE200808
Status Public on Apr 18, 2022
Title Temporal perturbation of histone deacetylase activity reveals a requirement for HDACs 1-3 in mes-endoderm cell differentiation
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We investigate the genome-wide chromatin landscape during mes-endoderm and cardiac progenitor specification to reveal dynamic changes to chromatin accessibility upon HDAC1-3 inhibition.
To evaluate the changes to chromatin accessibility upon inhibition of HDACs 1-3 during cardiac lineage specification, we performed ATAC-seq using the Omni-ATAC protocol (Corces et al., 2017) on Day 5 differentiated hiPSCs treated for 48 hours using small molecule HDAC inhibitors with isozyme selectivity
Overall design ATAC-seq analysis of cells at Day 5 of cardiac-directed hiPSC differentiation treated for 48 hours with HDAC inhibitors (1 µM MS275 and 1 µM BRD4884) (3 biological replicates per condition)
Contributor(s) Sinniah E, Naval-Sabchez M, Chen X, Nefzger C, Palpant NJ
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Submission date Apr 14, 2022
Last update date Apr 22, 2022
Contact name Nathan J. Palpant
Organization name University of Queensland
Street address 306 Carmody Rd
City Brisbane
State/province QLD
ZIP/Postal code 4067
Country Australia
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (9)
GSM6043947 Replicate 3; BRD4884 treated; Day 5 differentiated hiPSCs
GSM6043948 Replicate 2; BRD4884 treated Day 5 differentiated hiPSCs
GSM6043949 Replicate 1; BRD4884 treated Day 5 differentiated hiPSCs
BioProject PRJNA826850

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SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE200808_ATAC_seq_chromatin_regions.bed.gz 1.3 Mb (ftp)(http) BED
GSE200808_ATAC_seq_chromatin_regions.gtf.gz 1.6 Mb (ftp)(http) GTF
GSE200808_ATAC_seq_counts.txt.gz 2.1 Mb (ftp)(http) TXT
GSE200808_RAW.tar 7.6 Gb (http)(custom) TAR (of BW, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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