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| Status |
Public on Apr 05, 2024 |
| Title |
egr3 mutants 1 |
| Sample type |
SRA |
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| Source name |
Heart
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| Organism |
Danio rerio |
| Characteristics |
tissue: Heart
genotype: bns577-/-
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the miRNeasy micro Kit (Qiagen 217084), followed by on-column DNase digestion (DNase-Free DNase Set, Qiagen 79254), and final elution was performed in 12μl of RNase-free water
10ng total RNA was used for SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Data processing |
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides
Reads were aligned versus Ensembl zebrafish genome version danRer11 (Ensembl release 104) with STAR 2.7.10a
Aligned reads were filtered to remove: duplicates with Picard 2.27.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.30.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2) and batch corrected using CountClust (each biological replicate = one batch) (Dey K et al., Visualizing the structure of RNA-seq expression data using grade of membership models).
Genes were classified as significantly differentially expressed at average count > 5, multiple testing adjusted p-value < 0.05, and -0.585 < log2FC > 0.585.
Assembly: danRer11
Supplementary files format and content: libryr size notmalize amd batch corrected counts
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| Submission date |
Aug 30, 2023 |
| Last update date |
Apr 05, 2024 |
| Contact name |
Stefan Günther |
| E-mail(s) |
stefan.guenther@mpi-bn.mpg.de
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| Organization name |
MPI for heart and lung research
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| Street address |
ludwigtr. 43
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| City |
bad nauheim |
| ZIP/Postal code |
61231 |
| Country |
Germany |
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| Platform ID |
GPL30614 |
| Series (1) |
| GSE241935 |
Effect of egr3 knockout on gene expression of dissected zebrafish hearts |
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| Relations |
| BioSample |
SAMN37200092 |
| SRA |
SRX21533021 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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