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Status |
Public on Jul 01, 2020 |
Title |
3F3: Foot regeneration ATAC-seq, 3 hours post amputation, replicate 3 |
Sample type |
SRA |
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Source name |
Mid-Body Column Tissue
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Organism |
Hydra vulgaris |
Characteristics |
strain: 105 tissue: Mid-Body Column timepoint: 3 hours post amputation regeneration type: Foot Regeneration treatment: Untreated
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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.
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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.
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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)
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 4000 |
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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_Counts.Rdata) R data binary file containing the read counts in injury-responsive peaks for untreated 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. (untreated_consensus_diffbind_labels.bed) Bed file containing the consensus peakset for untreated 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. (untreated_deviations.csv) Average relative chromatin accessibility associated with transcription factor binding motifs for untreated ATAC-seq samples. Calculated using the R chromVAR package. (untreated_ATAC_Counts.csv) raw ATAC-seq read counts matrix for peaks in the untreated consensus peakset. Generated using the R DiffBind package. (3F3_final_shift.bw) 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. (3F_MG_final_shift.bw) 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 (https://research.nhgri.nih.gov/hydra/)
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Submission date |
Jun 22, 2020 |
Last update date |
Jul 01, 2020 |
Contact name |
Jack Cazet |
E-mail(s) |
jacazet@ucdavis.edu
|
Organization name |
University of California, Davis
|
Department |
MCB
|
Street address |
1 Shields Ave.
|
City |
Davis |
State/province |
CA |
ZIP/Postal code |
95616 |
Country |
USA |
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Platform ID |
GPL25712 |
Series (1) |
GSE152994 |
Oral Regeneration Is the Default Pathway Triggered by Injury in Hydra |
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Relations |
BioSample |
SAMN15342871 |
SRA |
SRX8598019 |