|
| Status |
Public on Nov 17, 2019 |
| Title |
ciona_oocyte |
| Sample type |
SRA |
| |
|
| Source name |
Ciona oocyte
|
| Organism |
Ciona savignyi |
| Characteristics |
cell type: oocyte
developmental stage: gamete
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The gametes and embryos were frozen at 70 below zero or subjected to immediate genomic extraction procedures. Genomic DNA was extracted by QIAamp DNA Mini Kit(QIAGEN) following the protocol of DNA Purification from Tissues with the cell lysis time adjusted depending on different samples.
Genomic DNA spiked with 0.5％ unmethylated Lambda DNA (Promega) was sonicated into 100-500bp. Fragmented DNA was then subjected to end repair,dA tailing, ligation with the end repair enzyme mix (NEB), Klenow 3´-5´ exo- (NEB) and T4 DNA ligase (NEB), respectively. Adapter-ligated DNA was recovered by 2％ agarose gel electrophoresis, and bisulfite conversion was performed using the EZ DNA methylation-Gold kit (Zymo Research) according to the instruction manual. Bisulfite-treated DNA was amplified with KAPA HiFi HotStart Uracil+ ReadyMix. Amplified DNA was recovered by 2％ agarose gel electrophoresis.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
3 replicates;replicate1[ciona_oocyte_rep1_*.fastq.gz];replicate2[ciona_oocyte_rep2_*.fastq.gz];replicate3[ciona_oocyte_rep3_*.fastq.gz]
|
| Data processing |
Adapters and low-quality reads were trimed with Trimmomatic
Reads alignment were performed with Bismark with default settings
duplicates were removed by deduplicate_bismark function of Bismark, and overlapped part of paired-end reads were removed by clipOverlap of bamUtil_1.0.9
methylation level were extracted with mpileup function of Samtools (v0.1.19)
Genome_build: sea_anemone[ASM20922v1];honey_bee[GCA_000002195.1];sea_urchin[Spur_3.1];ciona[CSAV2.0]
Supplementary_files_format_and_content: Format: bed; content: Methylation level for each CpG site plus 2 columns representing the numbers of Cs and Ts
|
| |
|
| Submission date |
Sep 29, 2015 |
| Last update date |
Nov 17, 2019 |
| Contact name |
jiang liu |
| E-mail(s) |
liuj@big.ac.cn
|
| Phone |
+8613621376393
|
| Organization name |
Beijing Institute of Genomics, Chinese Academy of Sciences
|
| Street address |
NO.1 Beichen West Road, Chaoyang District
|
| City |
beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL20966 |
| Series (1) |
| GSE73545 |
The evolution of DNA methylation inheritance and programming in animals |
|
| Relations |
| BioSample |
SAMN04122064 |
| SRA |
SRX1294712 |
