|
| Status |
Public on Nov 08, 2021 |
| Title |
lancelet_36hpf_embryo_hMeDIPseq |
| Sample type |
SRA |
| |
|
| Source name |
36 hpf lancelet embryo DNA subjected to hMeDIP-seq
|
| Organism |
Branchiostoma lanceolatum |
| Characteristics |
age: 36 hpf embryo
tissue: embryo
|
| Treatment protocol |
no treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
hMeDIP-seq library preparation for the DNA hydroxymethylation profiling was performed according to the Active Motif protocol (hMeDIP, Cat No 55010).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Library strategy: hMeDIP-seq
hMeDIP-seq raw data was processed using the NGSANE framework v0.5.2.0 (Buske et al, 2014). Sequenced hMeDIP-seq reads in fastq format were trimmed using Trimmomatic software (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:5:20).
Trimmed reads were mapped to Spur_v3.1, Bl71nemr and danRer10 reference genomes for sea urchin, lancelet and zebrafish, respectively, using bowtie2 v2.1.0 with the following parameters: bowtie2 --end-to-end -R 2 -p 10 -N 1 --very-sensitive -X 1000 --no-mixed --no-discordant (Langmead et al, 2012)
Optical and PCR duplicates were removed using Picard Tools’s function MarkDuplicates REMOVE_DUPLICATES=true.
Genome_build: sea urchin: Spur_v3.1; lancelet: Bl71nemr; zabrafish: danRer10
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Nov 06, 2021 |
| Last update date |
Nov 08, 2021 |
| Contact name |
Ksenia Skvortsova |
| E-mail(s) |
k.skvortsova@garvan.org.au
|
| Phone |
478135210
|
| Organization name |
Garvan Institute
|
| Department |
Genomics and Epigenetics
|
| Lab |
Developmental Epigenomics
|
| Street address |
384 Victoria St, Darlinghurst
|
| City |
Sydney |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL25186 |
| Series (2) |
| GSE188332 |
DNA hydroxymethylation profiling of purple sea urchin (Strongylocentrotus purpuratus), european lancelet (Branchiostoma lanceolatum) and zebrafish (Danio rerio) using hMeDIP-seq |
| GSE188334 |
Base-resolution 5-hydroxymethylcytosine maps of sea urchin and lancelet embryos and adult tissues |
|
| Relations |
| BioSample |
SAMN22959038 |
| SRA |
SRX13025538 |
