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Series GSE148935 Query DataSets for GSE148935
Status Public on Apr 14, 2021
Title LNCap cell nucleosome footprint elicits novel noncanonical GATA2 pioneer model
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Purpose: The dynamic nucleosome reorganization is the interplay among nucleosome and regulated by pioneer factors, which can access target DNA sequences on nucleosomes.The goals of this study are revealing the dynamic nucleosome footprint and how GATA2 is capable of resetting crowding array to primed, or accessible edge nucleosome states. Methods: LNCaP cells between passage number 30-35 were used for assay. cell nucleus was extracted, digested by MNase to Mono-nucleosome and ChIP/ChIP-exo was performed, the ChIP products were further used to generate library with illumina ChIP-seq kit. Hi-seq 3000 was used for sequencing and the data was analyzed by MACS2 for peaks. Results: GATA2 is associated with condensed nucleosome states and nucleosomes could unwrapped and be more accessible in pioneer factor GATA2 binding sites. Conclusions: Our study represents the first detailed nucleosome footprint of LNCap cells and analysis of the relationship between pioneer factor GATA2 and nucleosome reorganization in whole genomic DNA. These results demonstrated GATA2 play a critical role in an AR-independent manner in prostate cancer.
Overall design LNCaP cells was used as cell model, Mnase-seq and Mnase-ChIP-seq were applied for mono-nucleosome profiling and ChIP-exo of GATA2 compariing in vehicle and DHT conditions.
Contributor(s) Li T, Liu Q, Jin V
Citation(s) 35672415
Submission date Apr 20, 2020
Last update date Jun 23, 2022
Contact name Tianbao Li
Organization name University of Texas Health Science Center at San Anotnio
Department Molecular Medicine
Lab Victor Jin
Street address 7703 Floyd Curl
City San Antonio
State/province Texas
ZIP/Postal code 78229
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (44)
GSM4486239 GATA2_ChIP-exo_veh rep1
GSM4486240 GATA2_ChIP-exo_veh rep2
GSM4486241 MNase_veh rep1
BioProject PRJNA626583
SRA SRP257500

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Supplementary file Size Download File type/resource
GSE148935_RAW.tar 19.2 Gb (http)(custom) TAR (of BIGWIG)
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Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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