|
| Status |
Public on Jan 07, 2022 |
| Title |
4mC_DIP-seq_Av |
| Sample type |
SRA |
| |
|
| Source name |
whole animal
|
| Organism |
Adineta vaga |
| Characteristics |
strain: MBL
tissue: whole animal
medip antibody: N4-methyl-C (NEB)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extraction with Dneasy Tissue Kit (Qiagen). Sonication (Covaris S220) to obtain 200-400 bp range.
DNA library construction with NuGen Ovation Ultra Low System v2
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor sequence (cutadapt v1.9.2), and masked for short sequences (<15nt) or low-quality scores (<20), then mapped to reference genome using Bowtie, with default parameters and -n 1 -l 30
Aligned sequence reads processed with MACS using nomodel nolambda parameters
BigWig files were generated with deepTools2 using bamCoverage function
Supplementary_files_format_and_content: bed files with peak, BigWig files
|
| |
|
| Submission date |
Nov 06, 2019 |
| Last update date |
Jan 07, 2022 |
| Contact name |
Irina Arkhipova |
| E-mail(s) |
iarkhipova@mbl.edu
|
| Organization name |
Marine Biological Laboratory
|
| Department |
Josephine Bay Paul Center
|
| Lab |
Arkhipova Lab
|
| Street address |
7 MBL St
|
| City |
Woods Hole |
| State/province |
MA |
| ZIP/Postal code |
02543 |
| Country |
USA |
| |
|
| Platform ID |
GPL27728 |
| Series (2) |
| GSE140050 |
Non-canonical base modifications of bacterial origin in a eukaryotic genome [MeDIP-seq] |
| GSE140052 |
Non-canonical base modifications of bacterial origin in a eukaryotic genome |
|
| Relations |
| BioSample |
SAMN13226595 |
| SRA |
SRX7107223 |
