Zebrafish pineal gland light replica 2 - SRA

SRX363282: Zebrafish pineal gland light replica 2
1 ILLUMINA (Illumina HiSeq 2000) run: 5.1M spots, 1G bases, 626.3Mb downloads

Design: Adult (0.5-1.5 years old) Tg(aanat2:EGFP) zebrafish (Gothilf et al., 2002) were raised in a temperature controlled recirculation water system under 12-hr light: 12-hr dark (LD) cycles, and transferred to constant darkness (DD) at the end of the day prior to the experiment. Fish were exposed to a 1-hr light pulse (light intensity of 12 W/m2) prior to sampling (light treatment) or kept under constant darkness for control (dark treatment). The fish were anesthetized in 1.5mM Tricane (Sigma) and sacrificed by decapitation. Pineal glands were removed under a fluorescent dissecting microscope; the use of transgenic fish expressing enhanced green fluorescent protein (EGFP) in the pineal gland enabled its selective removal. The tissues were collected from light- and dark-treated fish at 6 time points with 4-hr intervals throughout one daily cycle, corresponding to CT2, 6, 10, 14, 18 and 22. For mRNA-seq, pineal glands were collected at the 6 sampling times and pooled together to establish triplicates of 15 pineal glands for every treatment. Total RNA for mRNA analysis was isolated using RNeasy Lipid Tissue Mini Kit (Qiagen). library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly, starting from total RNA, the messenger RNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Afterwards, the second strand was generated to create double-stranded cDNA. Finally, adapters were added by ligation to the double-stranded cDNA, which prepared the samples for cluster generation. After library quality check by Bioanalyzer High Sensitivity chip, clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow. Overall, 6 libraries (3 light groups and 3 dark groups) were run on one lane of an Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol (Institute of Applied Genomics, Italy). Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline (version 1.7). The reads were filtered using Illumina's HiSeq2000 softwares, Illumina indexes separation was also performed. On average, ~6.7 million paired-end reads were obtained for each library. The reads were of 2x100 base pairs.

Submitted by: TEL AVIV UNIVERSITY

Study: Danio rerio Transcriptome or Gene expression

PRJNA177642 • SRP016132 • All experiments • All runs

show Abstracthide Abstract

Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.

Sample: Zebrafish pineal gland

SAMN01765705 • SRS369337 • All experiments • All runs

Organism: Danio rerio

Library:

Instrument: Illumina HiSeq 2000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Spot descriptor:

1 forward102 reverse

Runs: 1 run, 5.1M spots, 1G bases, 626.3Mb

Run	# of Spots	# of Bases	Size	Published
SRR1048059	5,072,822	1G	626.3Mb	2013-12-12

ID:: 515719

SRA

Sequence Read Archive

Result Filters

Send to:

Supplemental Content

Related information

Recent activity