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Sample GSM6684538

Query DataSets for GSM6684538

Status

Public on Jul 01, 2024

Title

WTcal_3

Sample type

SRA

Source name

larvae

Organism

Danio rerio

Characteristics

tissue: larvae
genotype: WT
developmental stage: 72 hpf larvae

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

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

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

Submission date

Oct 26, 2022

Last update date

Jul 01, 2024

Contact name

Rahul N Kanadia

E-mail(s)

rahul.kanadia@uconn.edu

Phone

8604862692

Organization name

University of Connecticut