|
| Status |
Public on Jul 29, 2024 |
| Title |
ventricle, myd88-/-, untouched-2 |
| Sample type |
SRA |
| |
|
| Source name |
cardiac ventricles
|
| Organism |
Danio rerio |
| Characteristics |
tissue: cardiac ventricles
cell type: ventricular cells
genotype: myd88-/-
treatment: -
|
| Treatment protocol |
untouched ventricles or cardiac cryoinjury at 1 or 24 hours prior to heart extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from 3 pooled ventricles or 3 pooled injured tissues per sample using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-free DNase set, Qiagen) to avoid contamination by genomic DNA.
400ng of total RNA was used as input for VAHTS Stranded mRNA-seq Library preparation V6 following manufacture’s protocol (Vazyme).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides
Reads were aligned versus Ensembl zebrafish genome version danRer11 (Ensembl release 99) with STAR 2.7.3a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 2.21.7 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
The raw count matrix was normalized with DESeq2 version 1.26.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2). Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5, multiple testing adjusted p-value < 0.05, and -0.585 < log2FC > 0.585.
Gene counts were established with featureCounts 1.6.5 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 Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: DanRer11
Supplementary files format and content: library normilzed counts
|
| |
|
| Submission date |
Mar 21, 2024 |
| Last update date |
Jul 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 |
GPL30614 |
| Series (2) |
| GSE262169 |
The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration (dst139) |
| GSE262248 |
The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration |
|
| Relations |
| BioSample |
SAMN40568599 |
| SRA |
SRX24015861 |
