|
| Status |
Public on May 12, 2023 |
| Title |
Non-surgical control (NSC) nR181-L1-G7-P138 |
| Sample type |
SRA |
| |
|
| Source name |
esophageal tissue
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: esophageal tissue
age: 8-9 weeks
Sex: Male
time: NSC
treatment: Full thickness esophageal specimens were harvested in parallel from NSC
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA isolation was performed using Qiagen DNeasy Blood & Tissue kit (Qiagen) and genomic DNA was digested with MspI overnight. The digested products were size-selected using AMPure XP beads to remove anything above 300bp or small fragment retention.
DNA was bisulfite-converted using EZ DNA Methylation-Gold Kit (Zymo Research). The Accel-NGS Methyl-seq DNA library kit (Swift Biosciences) was used according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Non-surgical control (NSC)
RRBS
|
| Data processing |
Quality and adapter trimming of raw fastq files was executed using Trim Galore!0.6.6 with the following parameters: “--paired --clip_r1 10 --clip_r2 15 --three_prime_clip_r1 10 --three_prime_clip_r2 10 --fastqc”.
Reads were aligned to the rat genome (mRatBN7.2, data: 2020/11/10) by using Bismark 0.23.0
On average, 22.8 million trimmed reads per sample were aligned to rat genome (mRatBN7.2, release 105, Ensembl).
CpG sites were called using the “bismark_methylation_extractor” function (-- comprehensive option) in Bismark
Differential methylation cytosines (DMCs) were called analysis using methylKit (1.14.2) for CpGs with a minimum of 5 counts
Assembly: mRatBN7.2
|
| |
|
| Submission date |
May 14, 2022 |
| Last update date |
May 13, 2023 |
| Contact name |
Timothy Downing |
| E-mail(s) |
tim.downing@uci.edu
|
| Organization name |
UCI
|
| Department |
Department of Biomedical Engineering
|
| Lab |
Downing Lab
|
| Street address |
419 S. Circle View Drive
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE203028 |
DNA methylation dynamics during esophageal epithelial regeneration following repair with acellular silk fibroin grafts in rat |
|
| Relations |
| BioSample |
SAMN28408774 |
| SRA |
SRX15277801 |
