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| Status |
Public on Mar 28, 2017 |
| Title |
ddx39a_24hpf_RIPseq |
| Sample type |
SRA |
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| Source name |
embryos
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| Organism |
Danio rerio |
| Characteristics |
genotype: ddx39a mutant
tissue: embryo
developmental stage: 24hpf
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| Extracted molecule |
total RNA |
| Extraction protocol |
Microinjection ddx39a-Flag mRNA in ddx39a mutant embryos at one-cell stage. Lysates were clarified from 24hpf embryos were isolated with anti-Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
Magnetic beads with oligo(dT) were used to enrich the mRNAs, and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first-strand cDNA. Then double-stranded cDNA was synthesized by adding buffer solution, dNTPs and DNA polymeraseΙ. The double-stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions, then repaired at the tail ends, poly(A) added and enriched by PCR amplification. Finally, we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Illumina bcl2fastq2-v 2.16.0.10 software was used for base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Read quality was checked for each sample by using FastQC v 0.11.5.
High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters -q -p 8 --no-novel-juncs -G -o.
Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1.
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample
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| Submission date |
Mar 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuxi Yang |
| E-mail(s) |
yuxi.yang@smail.nju.edu.cn
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| Organization name |
Nanjing University
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| Department |
Medical School
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| Lab |
Xin Lou Lab
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| Street address |
Room 402, 12 Xuefu Road, Nanjing University
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210061 |
| Country |
China |
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| Platform ID |
GPL21741 |
| Series (1) |
| GSE97067 |
Transcriptome analysis on wild type and ddx39a mutant zebrafish embryos by Next Generation Sequencing |
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| Relations |
| BioSample |
SAMN06645144 |
| SRA |
SRX2674572 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2550918_ddx39a_24hpf_RIPseq_rawcount.txt.gz |
111.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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