|
Status |
Public on Dec 15, 2020 |
Title |
neuromasts_untreated_rep2 |
Sample type |
SRA |
|
|
Source name |
neuromasts_untreated_s
|
Organism |
Acipenser baerii |
Characteristics |
tissue: neuromasts neomycin treatment: untreated 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 |
SAMN15002946 |
SRA |
SRX8386201 |