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Sample GSM4566280 Query DataSets for GSM4566280
Status Public on Dec 15, 2020
Title neuromasts_12hpt_rep1
Sample type SRA
 
Source name neuromasts_12hpt_l
Organism Acipenser baerii
Characteristics tissue: neuromasts
neomycin treatment: 12 hour-post treatment (hpt)
development stage: 10 day-post hatching
Treatment protocol Eight samples were treated by 200 μM neomycin for 1 hour to deplete the hair cells, then tissues were collected on corresponding hpts
Growth protocol Larvae raised to stage 45 (10 day-post hatching) in artificial fresh water
Extracted molecule total RNA
Extraction protocol Total RNAs were extracted by TRIzol (Invitrogen) using standard protocols
RNA libraries were prepared by TruSeq RNA Sample Prep Kit (Illumina), following the manufacturer's instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing Basecalls performed using CASAVA version 1.8.2
Sequenced reads were cleaned by Trimmomatic-0.38: Remove illumina adapters.The first 13 bases were cutted from the start of reads. Bases below Q3 were cut off if at the beginning or end of a read. Reads were clipped starting from 5’ end, once average base quality below Q30 within a 40-bases sliding window. Reads were discarded if below 36 bases in length.
Reference transcriptome assembled by Trinity v2.6.6.
Cleaned reads of each sample were aligned to the annotated contigs using RSEM default procedures to to get gene counts
 
Submission date May 23, 2020
Last update date Dec 15, 2020
Contact name Jian Wang
E-mail(s) j_wang@shou.edu.cn
Organization name Shanghai Ocean University
Street address 999 Huchenghuan road, Pudong New Area
City Shanghai
ZIP/Postal code 201306
Country China
 
Platform ID GPL28574
Series (1)
GSE151096 Transcriptome profiles of sturgeon lateral line electroreceptor and mechanoreceptor during regeneration
Relations
BioSample SAMN15002945
SRA SRX8386202

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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