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Series GSE95651 Query DataSets for GSE95651
Status Public on Mar 03, 2017
Title Whole genome developmental time course of Tn5 transposon accessible chromatin patterns in sea urchin embryos
Organism Strongylocentrotus purpuratus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We have adapted ATAC-seq to sea urchin embryos. As a proof of concept, we documented strong ATAC-seq signals over the locations of a number of previously authenticated, developmentally active, cell type specific cis-regulatory modules. We then used the method to generate a systematic developmental series for embryos from three independent batches, obtained every six hours from blastula stage until completion of embryogenesis at 72h. The independent batches provide internal reproducibility controls.
 
Overall design In order to identify sites of active transcription through correlation of Tn5 accessible open chromatin with other genome feature, we collected embryos from three independent matings at 18 hour post fertilization (hpf), 24hpf, 30hpf, 50hpf, 60hpf and 70hpf. The nuclei were isolated and then processed by standard methods for Tn5 transposon binding. The subsequent labelled fragments were read on the Illumina latform and mapped to the genome.
 
Contributor(s) Vielmas E, Kudtarkar P, Antoshechkin I, Cameron RA
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Mar 02, 2017
Last update date Mar 20, 2017
Contact name Robert Andrew Cameron
E-mail parulk@caltech.edu
Organization name California Institute of Technology
Department Biology and Biological Engineering
Lab Center for Computational Regulator Genomics
Street address Caltech 1200 EAST CALIFORNIA BOULEVARD
City PASADENA
State/province CA
ZIP/Postal code 91125
Country USA
 
Platforms (1)
GPL20965 Illumina HiSeq 2500 (Strongylocentrotus purpuratus)
Samples (21)
GSM2520641 ATACseq_animal1_18hpf
GSM2520642 ATACseq_animal2_18hpf
GSM2520643 ATACseq_animal3_18hpf
Relations
BioProject PRJNA377768
SRA SRP101305

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
GSE95651_RAW.tar 5.1 Gb (http)(custom) TAR (of BED)
Raw data are available in SRA
Processed data provided as supplementary file

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