|
Status |
Public on May 12, 2023 |
Title |
Non-surgical control (NSC) nR181-L1-G7-P139 |
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 |
SAMN28408773 |
SRA |
SRX15277802 |