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Series GSE113191 Query DataSets for GSE113191
Status Public on May 17, 2018
Title CTCF boundary remodels chromatin domain and drives aberrant HOX gene transcription in acute myeloid leukemia
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary We analyzed RNA-seq, ATAC-seq, ChIP-seq and 4C-seq data to find that CTCF binding site located between HOXA7 and HOXA9 genes (CBS7/9) is critical for establishing and maintaining aberrant HOXA9-HOXA13 gene expression in AML. Disruption of the CBS7/9 boundary resulted in spreading of repressive H3K27me3 into the posterior active HOXA chromatin domain that subsequently impaired enhancer/promoter chromatin accessibility and disrupted ectopic long-range interactions among the posterior HOXA genes. Consistent with the role of the CBS7/9 boundary in HOXA locus chromatin organization, attenuation of the CBS7/9 boundary function reduced posterior HOTTIP lincRNA and HOXA gene expression and altered myeloid specific transcriptome profiles important for pathogenesis of myeloid malignancies.
Overall design We have submitted our RAW sequence datasets into SRA database (SRP115103 and Bioproject: PRJNA396046), including RNA-SEQ, ATAC-seq, ChIP-seq and 4C-seq for WT and CBS7/9KO MOLM13 leukemia cells
Contributor(s) Huang S, Luo H
Citation(s) 29760161
Submission date Apr 16, 2018
Last update date Mar 26, 2019
Contact name Suming Huang
Organization name Penn State University
Department Pediatrics
Street address 500 University Dr.
City Hershey
State/province PA
ZIP/Postal code 17033
Country USA
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (16)
GSM3099669 WT_1_RNAseq
GSM3099670 WT_2_RNAseq
GSM3099671 CBS79KO_1_RNAseq
BioProject PRJNA450401
SRA SRP140526

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE113191_RAW.tar 13.1 Mb (http)(custom) TAR (of BED, TXT)
GSE113191_WT-vs-CBS79KO_RNAseq_Differentially_expression_genes.txt.gz 27.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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