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Sample GSM7498268

Query DataSets for GSM7498268

Status

Public on Jun 24, 2023

Title

Sterlet sturgeon scute 26mm, replicate two

Sample type

SRA

Source name

cells of scute

Organism

Acipenser ruthenus

Characteristics

tissue: cells of scute
genotype: WT
measure: 26 mm

Extracted molecule

total RNA

Extraction protocol

RNAqueous kit (Ambion), prepared according to the manufacturer's instructions.
The libraries were built according to Illumina Standard Protocols.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

AR_scute_26mm_2
Sturgeon_scute_processed.txt

Data processing

In brief, every sterlet/bichir protein sequence was queried locally against the zebrafish proteome, following which regions with the longest alignment were matched to the respective zebrafish proteins.
Using this alignment-based approach, proteins with highest alignment percentage score were identified as orthologues.
Sterlet/bichir scute/scale RNA sequencing libraries were aligned to the sterlet/bichir sequences, while the zebrafish scale RNA sequencing libraries were aligned to the zebrafish sequences using Bowtie23.
Transcript counts were calculated using featureCounts and differential gene expression analysis was performed using DESeq2.
Using zebrafish gene annotations as a reference, we added the transcript counts for duplicated orthologues found in the sterlet/bichir genome to calculate an ‘aggregated’ transcript count for each gene as described by Martik et al., 2019.
These aggregated transcript counts were then normalized using the formula: Zi=Ti−min(T)/max(T)−min(T) whereZiis the normalized transcript count andTiis the absolute transcript count.
A subset of genes previously identified as being part of the neural crest gene regulatory network was then isolated from the count matrix and plotted as a heatmap using ComplexHeatmap package in Rstudio.
Assembly: Sterlet sturgeon (Genome assembly ASM1064508v1)/ Senegal bichir (Genome assembly ASM1683550v1)/ zebrafish (Genome assembly GRCz11)
Supplementary files format and content: tab-delimited text files that includes featurecounts values for each sample

Submission date

Jun 20, 2023

Last update date

Jun 24, 2023

Contact name

Jan Stundl

E-mail(s)

jstundl@caltech.edu

Organization name

California Institute of Technology

Lab

Bronner