RNA-Seq of the dorsal part of the bar region of the skin of Tropheus ... - SRA

SRX5775165: RNA-Seq of the dorsal part of the bar region of the skin of Tropheus duboisi Maswa
1 ILLUMINA (Illumina HiSeq 2500) run: 9.4M spots, 2.3G bases, 822.2Mb downloads

Design: To obtain a comprehensive list of transcripts from the bar regions of skin in T. duboisi, we performed library preparation step according to the protocol described by Standard TruSeq Stranded mRNA Sample Prep Kit (Illumina), on the RNA extractions. The samples used all had high RNA integrity (RIN > 7) and an RNA input of 1500ng for each sample was used for the library preparation. Next, we checked the quality of the libraries using D1000 ScreenTapes and reagents (Agilent) on a TapeStation 2200 (Agilent). The libraries were diluted based on an optimal quantity required for sequencing and then pooled equimolar. The sequencing was performed in the NGS Facility at Vienna Biocenter Core Facilities (VBCF, Austria) on one flowcell of an Illumina HiSeq2500, which generated 125bp paired-end reads. The demultiplexing of the raw reads was performed by the sequencing facility based on unique barcodes introduced in each sample during library preparation.

Submitted by: University of Graz

Study: Molecular players shaping a dorsally restricted colour pattern in Tropheus duboisi

PRJNA540663 • SRP194390 • All experiments • All runs

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The goal of this study is to profile the expression of genes involved in the formation of a dorsally restricted yellow bar pigmentation in adult Tropheus duboisi Maswa morph from Lake Tanganyika. As a proxy, we used another morph, Tropheus duboisi Kigoma, which displays similar vertical bar formation in on its body skin but without the dorsal bar yellow pigmentation observed in Maswa morph. This allows us to identify genes underlying the yellow bar colouration, as well as genes involved in dorsal bar restriction of the pigment pattern by comparing dorsal versus ventral bar regions in each morph.Our study provides the first transcriptional profile of yellow bar pigmentation in cichlids, and also the first list of xanthophore-related genes in a member of Tropheini cichlid tribe. In addition, the identified list of differentially expressed genes in the bar regions allowed us to hypothesize potential molecular players controlling the dispersal of xanthophores along the dorso-ventral body axis in teleost fish.

Sample: T. duboisi Maswa, dorsal part of the bar region of the skin, biological replicate 3

SAMN11552737 • SRS4708653 • All experiments • All runs

Organism: Tropheus duboisi

Library:

Name: 68324

Instrument: Illumina HiSeq 2500

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Runs: 1 run, 9.4M spots, 2.3G bases, 822.2Mb

Run	# of Spots	# of Bases	Size	Published
SRR8996273	9,388,945	2.3G	822.2Mb	2019-05-01

ID:: 7765668

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