GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM4632729 Query DataSets for GSM4632729
Status Public on Jul 01, 2020
Title 3iF5: Foot regeneration ATAC-seq, 3 hours post amputation, replicate 5, iCRT14 treated
Sample type SRA
Source name Mid-Body Column Tissue
Organism Hydra vulgaris
Characteristics strain: 105
tissue: Mid-Body Column
timepoint: 3 hours post amputation
regeneration type: Foot Regeneration
treatment: treated with 5uM iCRT14 for 5 hours
Treatment protocol For iCRT14 treatment, Hydra were pre-incubated in 5uM iCRT14 for two hours prior to amputation. Following amputation, iCRT14 treatment continued until tissue was collected for library preparation.
Growth protocol Hydra vulgaris strain 105 polyps were cultured according to standard protocol (Lenhoff, 1983) at 18˚C and fed 1-2 times weekly with Artemia nauplii.
Extracted molecule genomic DNA
Extraction protocol 15 regenerating tips were homogenized using a dounce homogenizer and cells were lysed using a cocktail of mild detergents as described in the OMNI-ATAC-seq protocol (Corces et al., 2017). ~50000 nuclei were then spun down and used for tagmentation.
Libraries were prepared as described in the original ATAC-seq publication (Buenrostro et al., 2013)
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
Data processing Low quality base calls and adapter sequences were removed using trimmomatic (V. 0.36) with the following settings: PE -threads 16 -phred33 ILLUMINACLIP:adapterFile.fa:2:30:10:2:true TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32. Reads were then mapped to the Hydra vulgaris 2.0 genome using bowtie2 (V. 2.2.6) with the following settings: -X 1000 --very-sensitive-local --mm. Trimmed reads were also mapped to the Hydra vulgaris mitochondrial genome using identical settings. Reads that mapped to the mitochondrial reference were then filtered from genome-mapped reads using the Picard Tools (V. 2.17.8) function FilterSamReads using the FILTER=excludeReadList parameter. Reads with a MAPQ value < 3 as well as incoherently mapped read pairs were removed using samtools (V. 1.2) using the following parameters: view -Su -F 524 -q 3. PCR duplicates were then identified using the Picard Tools MarkDuplicates function using default settings. Duplicate read pairs were then removed using samtools view -F 1804. Finally, reads were shifted to compensate for the offset in tagmentation site relative to the tn5 binding site using the deeptools (V. 3.3.1) alignmentSieve function with the --ATACshift flag.
processed data files format and content: (chromVar_iCounts.Rdata) R data binary file containing the read counts in injury-responsive peaks for all ATAC-seq samples. Used to identify changes in average accessibility associated with predicted transcription factor binding sites. Peak width was fixed at 250 bp. Generated using the R chromVAR package. (full_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for all ATAC-seq samples. Peaks were included in the consensus peakset if they passed an IDR threshold of 0.1 in at least three pairwise comparisons for at least one treatment group. (full_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for all ATAC-seq samples. Calculated using the R chromVAR package. (full_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the full consensus peakset. Generated using the R DiffBind package. ( Bigwig file of ATAC-seq read density for the specified individual biological replicate aligned to the Hydra vulgaris 2.0 genome. Read density was calculated using a 10bp window. Generated using deeptools. ( Bigwig file of ATAC-seq read density for pooled biological replicates in the specified treatment group. Read density was calculated using a 10bp window. Generated using deeptools.
Genome_build: Hydra vulgaris 2.0 genome (
Submission date Jun 22, 2020
Last update date Jul 01, 2020
Contact name Jack Cazet
Organization name University of California, Davis
Department MCB
Street address 1 Shields Ave.
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
Platform ID GPL25712
Series (1)
GSE152994 Oral Regeneration Is the Default Pathway Triggered by Injury in Hydra
BioSample SAMN15342915
SRA SRX8598056

Supplementary file Size Download File type/resource 119.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap