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| Status |
Public on Oct 03, 2024 |
| Title |
Bisufite, Intestine, FA |
| Sample type |
SRA |
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| Source name |
Rainbow trout Intestine
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| Organism |
Oncorhynchus mykiss |
| Characteristics |
cell type: Rainbow trout Intestine
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
20–30 mg of tissue powder was cross-linked with 1% formaldehyde for 8 minutes, and quenched for 10 minutes with 100 μl of glycine. Centrifugation at 2000 g for 5 min yielded the nuclei, which were then resuspended in 600 μl of iS1 buffer and incubated for 30 min on ice. Depending on the tissues, the Bioruptor Pico sheared chromatin between 10 and 15 cycles.
Libraries were constructed using the NEBNext Ultra DNA library prep kit (New England Biolabs #E7645L, Ipswich, MA)
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Methyl-MiniSeq
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| Data processing |
The raw sequencing data was subjected to quality control using FastQC (version v0.11.8). Adapter sequences were removed from the reads using trim galore (version 0.6.4) (https://github.com/FelixKrueger/TrimGalore).
Trimmed reads were aligned to the rainbow trout reference genome using Bowtie2 (version 2.3.5.1) with the "--end-to-end" and "--very-sensitive" parameters.
The aligned reads were stored in BAM format for subsequent analysis. MACS3 (Model-based Analysis of ChIP-Seq 3) (version 3.0.0a6) was used for peak calling. The aligned reads in BAM format were utilized as input, and specific parameters were adjusted for each histone modification. For H3K27me3, which represents broad peaks, we set the q-value threshold to 0.05. For the rest of the histone modifications, which represent narrow peaks, we set the q-value threshold to 0.01.
Assembly: GCF_013265735.2
Supplementary files format and content: bed, narrowPeak (except for Input sample)
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| Submission date |
Apr 18, 2024 |
| Last update date |
Oct 03, 2024 |
| Contact name |
Rafet Al-Tobasei |
| E-mail(s) |
rafet.al-tobasei@mtsu.edu
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| Organization name |
Middle Tennessee State University
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| Department |
Computer Science Department
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| Street address |
358 KOM
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| City |
Murfreesboro |
| State/province |
TN |
| ZIP/Postal code |
37132 |
| Country |
USA |
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| Platform ID |
GPL24430 |
| Series (1) |
| GSE245212 |
Epigenomic maps of the rainbow trout reveal epiQTL signatures of genetic selection and regulatory elements involved in controlling gene expression and genome evolution |
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| Relations |
| BioSample |
SAMN41008114 |
| SRA |
SRX24301429 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8215885_Intestine_1_R1_val_1_bismark_bt2_pe.bismark.cov.gz |
78.8 Mb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
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