|
| Status |
Public on Aug 28, 2020 |
| Title |
ATAC-Seq T1L3 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Salmo salar |
| Characteristics |
timepoint: T1
|
| Treatment protocol |
Fish from a single management group were sacrificed at a timepoint immediately before initiation of the long-light regime (throughout referred to as T1) and at three timepoints afterwards (T2, T3 and T4).
|
| Growth protocol |
Fish were managed in a tank based experimental system to facilitate a long-light photoperiod regime known to stimulate the onset of sexual maturation
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue samples from liver were snap frozen in liquid Nitrogen and preserved at -80 °C. Frozen tissue (20 mg) was ground in liquid nitrogen using a mortar and pestle. The pulverized tissue was transferred to a pre-chilled 2 ml dounce homogenizer containing 1mL cold 1x homogenisation buffer and homogenised with the pestle until a uniform suspension was seen (10-20 strokes). The homogenate was filtered with a 40uM nylon cell strainer (BD Falcon) before layering onto the iodixanol solution as described previously (Corces et al., 2017). The ratio of nuclei to enzyme concentration was optimised for each sample by performing transposition reactions containing 50000, 100000 and 200000 nuclei with 2.5ul of tagment enzyme in 50ul of transposition mix (Corces et al., 2017). The transposed DNA was amplified with custom primers as described (Buenrostro et al., 2015).
12 liver ATAC-seq libraries arising from 3 biological replicates x 4 time points (T1-T4) were sequenced at IMB sequencing facility (University of Queensland) on an Illumina NextSeq 150 cycle (2X 75 bp).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Liver T1 library biol. rep. 3
|
| Data processing |
Raw reads were mapped to the Atlantic salmon reference genome ICSASG_v2 (Lin et al., 2016) using BOWTIE2 version 2.3.5.1 with the --very-sensitive parameter (Langmead & Salzberg, 2012). Duplicate reads were removed using the MarkDuplicates function in Picard (http://broadinstitute.github.io/picard/). Multi-mapped reads and mitochondrial reads were filtered and only uniquely mapped reads (MAPQ > 10) were extracted from alignment files using SAMTOOLS for downstream analyses
For peak calling, the model-based analysis of ChIP-Seq (MACS2) (https://github.com/macs3-project/MACS) was used to identify read enrichment regions “peaks” using default parameters. Only peaks detected in at least two replicates per condition were used for downstream analyses. Peaks for all of the time points were merged together to a unique peak list per tissue. The number of raw reads mapped to each peak was quantified using the Python package HTSeq version 0.11.1 (Anders et al., 2015).
Samples from the long photoperiod time points (T2, T3 and T4) were compared to control samples (T1) for each tissue. Raw counts were analysed to infer differential accessible chromatin using the R package edgeR. P-values were corrected for multiple testing using the Benjamini and Hochberg algorithm. Peaks with FDR < 0.05 and log2FC ± > 1 were considered significantly differentially accessible regions (DARs).
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000233375.1
Supplementary_files_format_and_content: Matrix table with raw counts per peak for all samples
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample
|
| |
|
| Submission date |
Aug 27, 2020 |
| Last update date |
Aug 28, 2020 |
| Contact name |
Amin Roushdy Mohamed |
| E-mail(s) |
am_rd85@yahoo.com
|
| Organization name |
CSIRO
|
| Department |
Agriculture and Food
|
| Lab |
Aquaculture Genomics
|
| Street address |
306 Carmody Rd, University of Queensland
|
| City |
Brisbane |
| State/province |
Queensland |
| ZIP/Postal code |
4067 |
| Country |
Australia |
| |
|
| Platform ID |
GPL28848 |
| Series (2) |
| GSE156998 |
Liver Chromatin accessibility landscapes during onset of salmon maturation |
| GSE157003 |
Multiomics profiling during onset of Salmon maturation |
|
| Relations |
| BioSample |
SAMN15924930 |
| SRA |
SRX9024658 |
