|
Status |
Public on Nov 02, 2018 |
Title |
Replicate 3 - 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-3 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 |
SAMN10267719 |
SRA |
SRX4913461 |