|
| Status |
Public on Jun 01, 2021 |
| Title |
SM_Telecephlon |
| Sample type |
SRA |
| |
|
| Source name |
Telecephlon
|
| Organism |
Silurus meridionalis |
| Characteristics |
tissue: Telecephlon
developmental stage: adult
|
| Growth protocol |
Use adult sample from benthic environment
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from each sample using Trizol Reagent (Invitrogen, Carlsbad, CA, U.S.A) according to the manufacturer’s instructions. The extracted RNA was further treated with DNaseⅠ (RNase-free 5 U/mL) to eliminate genomic DNA contamination. Poly (A) + mRNA was purified using the DynaBeads mRNA Purification kit (Life Technologies).
Paired-end cDNA libraries were constructed using the RNA Seq NGS Library Preparation Kit for Whole-Transcriptome Discovery (Gnomegen).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
RNAseq from tissue:Telecephlon
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to referenced genome using histat2 (version 2.1.0)
StringTie 1.3.4d were used to calculate FPKM
bam_to_bigwig(https://github.com/hotdogee/bam_to_bigwig) were used to produce bigWig
Genome_build: under Bioproject : PRJNA427243; See also SM.tbl.txt for transcriptome annotation.
Supplementary_files_format_and_content: bigwig and text file with FPKM.
|
| |
|
| Submission date |
Jun 14, 2018 |
| Last update date |
Jun 01, 2021 |
| Contact name |
Fan ding ding |
| E-mail(s) |
biocomfun@qq.com
|
| Organization name |
EasyATCG
|
| Street address |
yantian shashen Road
|
| City |
Shenzhen |
| ZIP/Postal code |
808583 |
| Country |
China |
| |
|
| Platform ID |
GPL25184 |
| Series (1) |
| GSE115804 |
Tissues' transcriptome sequence of Silurus meridionalis |
|
| Relations |
| BioSample |
SAMN09269385 |
| SRA |
SRX4130682 |
