|
| Status |
Public on Apr 29, 2024 |
| Title |
sample1: zebrafish strain AB, DMSO |
| Sample type |
SRA |
| |
|
| Source name |
Whole-larvae treated from 3 to 6 dpf with DMSO (0.1%)
|
| Organism |
Danio rerio |
| Characteristics |
strain: AB
genotype: Wild type
age: Larvae of 6 dpf
tissue: Whole-larvae
treatment: DMSO (0.1%)
|
| Treatment protocol |
Zebrafish larvae were exposed to 1 μM BaP or 0.1% DMSO from 3 to 6 dpf
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 4 pooled biological replicates using NZYol (NZYTech, Lisbon, Portugal).
200 ng of total RNA was used as input for VAHTS Stranded mRNA-seq Library preparation following manufacture’s protocol (Vazyme).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Trimmomatic version 0.38 was employed to trim reads after a quality drop below a mean of Q20 in a window of 5 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl zebrafish genome version DanRer11 (GRCz11.92) using STAR 2.6.1d with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% .
The number of reads aligning to genes was counted with featureCounts 1.6.3 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Genome_build: DanRer11
Supplementary_files_format_and_content: library size normalized counts
|
| |
|
| Submission date |
May 17, 2021 |
| Last update date |
Apr 29, 2024 |
| Contact name |
Stefan Günther |
| E-mail(s) |
stefan.guenther@mpi-bn.mpg.de
|
| Organization name |
MPI for heart and lung research
|
| Street address |
ludwigtr. 43
|
| City |
bad nauheim |
| ZIP/Postal code |
61231 |
| Country |
Germany |
| |
|
| Platform ID |
GPL20828 |
| Series (1) |
| GSE174529 |
New insights into benzo[⍺]pyrene osteotoxicity in zebrafish |
|
| Relations |
| BioSample |
SAMN19231649 |
| SRA |
SRX10909283 |
