RNA-Seq of Boleophthalmus pectinirostris: kidney - SRA

SRX6533024: RNA-Seq of Boleophthalmus pectinirostris: kidney
1 ILLUMINA (Illumina HiSeq 4000) run: 23.9M spots, 7.2G bases, 2.5Gb downloads

Design: Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0. Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA,which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs,The ligated products are amplified with PCR by the following conditions: initial denaturation at 95 for 3 min; 8cycles of denaturation at 98 for 15 sec, annealing at 60 for 15 sec, and extension at 72 for 30 sec; and then final extension at 72 for 5 min. The average insert size for the final cDNA library was 300 bp (50 bp). At last, we performed the 150bp paired-end sequencing on an Illumina Hiseq 4000 (LC Bio, China) following the vendor's recommended protocol.

Submitted by: Ningbo University

Study: Boleophthalmus pectinirostris Transcriptome or Gene expression

PRJNA543702 • SRP216151 • All experiments • All runs

show Abstracthide Abstract

Changes in oxygen concentration affect the normal physiological activities of the animal, but Mudskipper (Boleophthalmus pectinirostris) inhabit aquatic and terrestrial habits where oxygen concentndant and diverse pathogenic microorganisms, they are rarely challenged by severe barations differ widely. Although mudskippers inhabit intertidal mudflats containing abucterial diseases. Therefore, investigating the effects of hypoxic stress and Edwardsiella tarda infection on the innate immune system of mudskipper is very promising.

Sample: The DG2 group was treated with cobalt chloride (CoCl2) for 8 hours and then delayed Edwardian bacteria for 5 hours

SAMN11658166 • SRS5144134 • All experiments • All runs

Organism: Boleophthalmus pectinirostris

Library:

Name: DG2

Instrument: Illumina HiSeq 4000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: PolyA

Layout: PAIRED

Runs: 1 run, 23.9M spots, 7.2G bases, 2.5Gb

Run	# of Spots	# of Bases	Size	Published
SRR9771480	23,866,581	7.2G	2.5Gb	2020-06-30

ID:: 8636640

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