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Sample GSM3440171 Query DataSets for GSM3440171
Status Public on Nov 02, 2018
Title Replicate 2 - ATACseq reads generated for whole homeostatic Hydra
Sample type SRA
 
Source name Hydra vulgaris 105 (nuclei)
Organism Hydra vulgaris
Characteristics strain: Hydra vulgaris 105
tissue: whole animal
Growth protocol Hydra vulgaris 105 were cultured according to standard protocol (Lenhoff, 1983) at 18˚C.
Extracted molecule genomic DNA
Extraction protocol 5 whole Hydra were homogenized using a dounce homogenizer and cells were lysed using a cocktail of mild detergents. ~50000 nuclei were then spun down and used for tagmentation.
OMNI-ATACseq (Corces et al. 2017)
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description ATAC-2
processed data file: consensus_peak.bed
Data processing Nextera adapters and unpaired reads were removed using trimmomatic 0.36. Reads were mapped using bowtie 2.2. PCR duplicates were removed using Picard 2.17.8. Peaks were called using MACS2 2.1.1.
genome build: Hydra vulgaris 2.0 genome (https://research.nhgri.nih.gov/hydra/)
Supplementary_files_format_and_content: Bed file. Consensus peak list consisting of all peaks that passed an IDR threshold of 0.1 for at least one pairwise comparison among the three biological replicates
 
Submission date Oct 22, 2018
Last update date Jul 30, 2019
Contact name Celina E Juliano
E-mail(s) cejuliano@ucdavis.edu
Organization name University of California Davis
Department MCB
Lab Julianolab
Street address 149 Briggs Hall
City Davis
State/province California
ZIP/Postal code 95616
Country USA
 
Platform ID GPL25712
Series (1)
GSE121617 Stem cell differentiation trajectories in Hydra resolved at single cell resolution
Relations
BioSample SAMN10267720
SRA SRX4913460

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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