|
| Status |
Public on May 29, 2024 |
| Title |
RNAseq_StdMO |
| Sample type |
SRA |
| |
|
| Source name |
dome
|
| Organism |
Danio rerio |
| Characteristics |
tissue: dome
genotype: Wild type
treatment: Std-MO injection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by TRIzol method and integrity was assessed using the Fragment Analyzer 5400.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer' s recommendations.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore (version 0.6.7).
Trimmed sequence reads were mapped to danRer7 using HISTAT2 (version 2.2.1) with default parameters.
Raw counts for the feature of genes were extracted by featureCounts (version 2.0.3).
BigWig files were generated by using deepTools (version 2.4.2)
danRer7
Tab-delimited text files include features' raw counts for each sample
|
| |
|
| Submission date |
Jun 02, 2023 |
| Last update date |
May 29, 2024 |
| Contact name |
li kuan |
| E-mail(s) |
likuan@cibr.ac.cn
|
| Organization name |
Tsinghua University
|
| Street address |
zhongguancun
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL24995 |
| Series (1) |
| GSE183453 |
R-loop landscapes during parental-to-zygotic transition in zebrafish |
|
| Relations |
| BioSample |
SAMN35572843 |
| SRA |
SRX20580020 |
