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Series GSE76006 Query DataSets for GSE76006
Status Public on Oct 05, 2016
Title ATAC-Se1 to investigate the spatial choreography of the accessible genome
Organism Homo sapiens
Experiment type Other
Summary In order to completely understand the spatial choreography of the accessible genome in the 3D intact nucleus, we had developed a new technique termed assay of transposase accessible chromatin by visualization (ATAC-see). In brief, we had labeled the adaptor in hypersensitive Tn5 transposase with fluorophore dye and performed the Tn5 tagmentation on the fixed culture cells slide. We had performed ATAC-see in different types of cells and found out there are cell types specific spatial choreography of the accessible genome in the 3D intact nucleus, which is tightly linked to cell types specific function. Importantly, we could images the open chromatin distribution and do the sequencing on the exactly same sample, which offer a powerful tool to understand how the open chromatin organize in the 3D nucleus and how the open chromatin regulate gene expression.
Overall design We had compared the ATAC-seq libraries under different conditions such as with different Tn5s (Illumina Nextera Tn5, home-made Tn5 with and without Atto labeled on the adaptors in GM12878 cells), with and without fixation (in HT1080 cells ) and the cells growing on different materials (growing HT1080 cells on slide and suspensions cells in the tubes). In addition, we had performed ATAC-seq in human neutrophil.
Contributor(s) Chen X, Shen Y, Chang HY
Citation(s) 27749837
Submission date Dec 14, 2015
Last update date May 15, 2019
Contact name Xingqi Chen
Organization name Stanford University
Lab Howard Chang's lab
Street address 269 Campus Drive
City Palo Alto
State/province CA
ZIP/Postal code 94305-5168
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (22)
GSM1972141 GM12878_Illumina_Tn5_rep1
GSM1972142 GM12878_Illumina_Tn5_rep2
GSM1972143 GM12878_home_made_Atto_Tn5_rep1
BioProject PRJNA305986
SRA SRP067388

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Supplementary file Size Download File type/resource
GSE76006_RAW.tar 20.3 Gb (http)(custom) TAR (of BED)
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Raw data are available in SRA
Processed data provided as supplementary file

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