|
| Status |
Public on Mar 01, 2019 |
| Title |
Dev4D |
| Sample type |
SRA |
| |
|
| Source name |
4dpf
|
| Organism |
Oreochromis niloticus |
| Characteristics |
developmental period: Embryo
Stage: Pharyngula
strain: Chitralada
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruseqTM Small RNA Preparation kit was used for the construction of small RNA sequencing libraries, following manufacture's protocol.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
microRNA sequencing
|
| Data processing |
Base-calling was performed using Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70).
Adaptor sequences were trimmed. FASTQ files were converted into FASTA with a custom Perl script. Reads were counted, collapsed to unique reads and filtered using the UEA small RNA Workbench. Reads were exactly matched to tilapia genome (Orenil1.1v) with PatMaN
Precursors from miRBase were searched against the tilapia genome using BLAST. Novel tilapia miRNA loci were predicted with both miRCat 79 and miRDeep2
An in-house Python pipeline selected matched reads from each precursor locus and estimated the read counts by weight count (raw read count divided by number of precursor locus aligned).
Reads were normalized by DESeq method for miRNA 5p and 3p using Bioconductor package in R
Genome_build: Orenil 1.1
Supplementary_files_format_and_content: counts
|
| |
|
| Submission date |
Aug 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Danillo Pinhal |
| E-mail(s) |
[email protected]
|
| Organization name |
Sao Paulo State University
|
| Department |
Genetics
|
| Lab |
Laboratory Genomics and Molecular Evolution
|
| Street address |
R. Prof. Dr. Antonio C. W. Zanin s/n
|
| City |
Botucatu |
| State/province |
SP |
| ZIP/Postal code |
18618689 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL23168 |
| Series (1) |
| GSE102878 |
Genome-wide microRNA screening in Nile tilapia reveals pervasive transcription of isomiRs, sex-biased arm switching and increasing complexity of expression throughout development |
|
| Relations |
| BioSample |
SAMN07523012 |
| SRA |
SRX3110675 |
