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| Status |
Public on Jul 01, 2024 |
| Title |
cal_3 |
| Sample type |
SRA |
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| Source name |
larvae
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| Organism |
Danio rerio |
| Characteristics |
tissue: larvae
genotype: Clbns846
developmental stage: 72 hpf larvae
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from pools of genotyped 72-hour post fertilization (hpf) larvae using TRIzol
Poly(A)-enriched RNA was used to generate cDNA libraries and sequenced using the Illumina HiSeq by the Australian Genomics Research Facility (AGRF), yielding 100bp single end reads
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Reads were aligned to the GRCz11 Ensembl v99 genome assembly using Hisat2
Retention and alternative splicing analysis was then performed as described before (Baumgartner et al., 2018; Olthof et al., 2019). Briefly, unspliced reads that aligned to exon-intron boundaries of introns of interest were quantified using BEDTools. These counts were utilized to calculate a mis-splicing index (MSI), by dividing them to the total number of spliced reads aligning to the annotated exon-exon boundary. Only introns that passed the filtering criteria (> 4 exon-intron boundary reads, ≥1 read aligning to both the 5′ and 3′ splice site, > 95% intron coverage) in at least one replicate were considered retained.
Assembly: GRCz11 Ens. V.99
Supplementary files format and content: Tab-delimited txt file with MSI values
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| Submission date |
Oct 26, 2022 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Rahul N Kanadia |
| E-mail(s) |
rahul.kanadia@uconn.edu
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| Phone |
8604862692
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| Organization name |
University of Connecticut
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| Department |
Physiology and Neurobiology
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| Street address |
75 N. Eagleville Road
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| City |
Storrs |
| State/province |
CT |
| ZIP/Postal code |
06269 |
| Country |
USA |
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| Platform ID |
GPL18413 |
| Series (1) |
| GSE216619 |
Taxonomy of introns, their evolution, and the role of minor introns in stress response |
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| Relations |
| BioSample |
SAMN31461444 |
| SRA |
SRX18031494 |
| 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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