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| Status |
Public on Jul 11, 2024 |
| Title |
Wild-type zebrafish atrial cardiomyocytes, 72 hours post fertilization, rep 3 |
| Sample type |
SRA |
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| Source name |
embryonic heart
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| Organism |
Danio rerio |
| Characteristics |
tissue: embryonic heart
cell type: cardiomyocyte
genotype: wild-type
treatment: 72 hours post fertilization
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| Extracted molecule |
total RNA |
| Extraction protocol |
miRNeasy micro Kit (Qiagen), using low input DNase protocol
Approximately 1ng of total RNA was used as starting material for SMART®-Seq HT 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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| Description |
AC-72h_3
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| 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 (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl zebrafish genome version danRer11 (Ensembl release 104) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.0.0 (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 2.0.4 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).
Assembly: danRer11
Supplementary files format and content: count matrix
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| Submission date |
Dec 01, 2023 |
| Last update date |
Jul 11, 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) |
| GSE249149 |
Identification of genes important during atrial myocardial morphogenesis |
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| Relations |
| BioSample |
SAMN38564919 |
| SRA |
SRX22707800 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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