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| Status |
Public on Aug 07, 2019 |
| Title |
WT 3hpf m5C rep1 |
| Sample type |
SRA |
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| Source name |
Zebrafish embryo
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| Organism |
Danio rerio |
| Characteristics |
strain: AB strain
cell type: Zebrafish embryo
age: 3 hpf
tissue: whole embryo
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent (Ambion). mRNA was extracted with using Dynabeads® mRNA Purification Kit (Ambion) and subjected to TURBO™ DNase (Invitrogen) treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA-BisSeq library construction.
Thus purified mRNA was used for RNA-BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 (Dhfr mRNA serves as methylation conversion control) was fragmented to ~100-nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent (Ambion), then stopped by 10× RNA stop solution (Ambion), and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution (pH 5.1), which is a 100:1 mixture of 40% sodium bisulfite (Sigma) and 600 µM hydroquinone (Sigma) and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns (PALL Corporation) with centrifugation. After washed with nuclease-free water and centrifuged for five times, the RNA was finally disolved in 75 μl nuclease-free water and then desulfonated by incubation with an equal volume of 1 M Tris-HCl (pH 9.0) at 75 °C for 1 h. After ethanol precipitation, the RNA was resuspended in 11 µl of RNase-free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase (Invitrogen) and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA-Seq Kit (KAPA) according to the manufacturer’s instructions.Libraries were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 125 bp.
RNA-BisSeq
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
WT 3hpf rep1
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| Data processing |
Reads were aligned to the zv9 and hg19 genome assembly using meRanTK v1.2.0
m5C sites were called by meRanCall v1.2.0 and annotated by applying BEDTools’ intersectBed.
Genome_build: zv9 and hg19
Supplementary_files_format_and_content: m5C sites in two biological replicates.
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| Submission date |
Sep 28, 2018 |
| Last update date |
Aug 07, 2019 |
| Contact name |
Bao-Fa Sun |
| E-mail(s) |
sunbf@big.ac.cn
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| Organization name |
Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)
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| Street address |
Da-Tun Road
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| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL18413 |
| Series (1) |
| GSE120645 |
m5C profiles in zebrafish embryo sample. |
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| Relations |
| BioSample |
SAMN10144063 |
| SRA |
SRX4776890 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3406891_WT_3hpf_rep1_m5C.txt.gz |
94.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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