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| Status |
Public on Apr 15, 2020 |
| Title |
Q96K97del_3_PairF [5F1Lardelli_2] |
| Sample type |
SRA |
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| Source name |
Clutch of larvae
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| Organism |
Danio rerio |
| Characteristics |
genotype: psen1Q96_K97del/+
developmental stage: larvae
age: 7 days post-fertilization
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| Growth protocol |
The larvae were raised in E3 medium for 7 days, allowing complete larval yolk absorption but not food intake
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from pooled larvae using the mirVanaTM miRNA isolation Kit (Ambion, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA). DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA-freeTM Kit (Ambion, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA). PolyA amplification was performed for the construction of sequencing libraries.
Demultiplexed libraries were provided by the sequencing centre at SAHMRI as 75bp single-end reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
5F1Lardelli_2
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| Data processing |
Illumina BaseSpace was used for base-calling.
Reads were trimmed using AdapterRemoval v2.2.1 setting a minimum quality of 30 and a minimum length of 35.
Trimmed reads were aligned to the Danio rerio genome Ensembl Release 96 (GRCz11) using STAR v2.5.3a.
FeatureCount was used to count the align reads assigned to each gene, specifying that only unique alignments which strictly overlapped exonic regions were counted.
Genome_build: GRCz11
Supplementary_files_format_and_content: An output file was generated from FeatureCount containing the gene counts of all samples.
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| Submission date |
Apr 14, 2020 |
| Last update date |
Apr 15, 2020 |
| Contact name |
Stephen Martin Pederson |
| E-mail(s) |
stephen.pederson@adelaide.edu.au
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| Phone |
+614 1333 9618
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| Organization name |
University of Adelaide
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| Department |
Biological Sciences
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| Lab |
Boinformatics Hub
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| Street address |
North Terrace
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| City |
Adelaide |
| State/province |
SA |
| ZIP/Postal code |
5005 |
| Country |
Australia |
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| Platform ID |
GPL20828 |
| Series (1) |
| GSE148631 |
Transcriptome analyses of 7-day-old zebrafish larvae possessing a familial Alzheimer’s disease-like mutation in psen1 indicate effects on oxidative phosphorylation, mcm functions, and iron homeostasis. |
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| Relations |
| BioSample |
SAMN14595797 |
| SRA |
SRX8112207 |
| 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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