|
| Status |
Public on Apr 10, 2017 |
| Title |
Liver T3 2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver T3 2
|
| Organism |
Oreochromis niloticus |
| Characteristics |
tissue: Liver
age: Juvenil (4 month)
treatment: T3 25 nM 12 h
|
| Treatment protocol |
All fish treatments were performed following an immersion protocol and treatment conditions were 25 nM of T2 or T3 and 12 h of exposure
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from brain regions and liver tissues with TRIzol (Invitrogen)
Libraries were generated using Illumina TruSeq RNA Sample Preparation Kit according to the manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Quality Control (QC) of raw reads was performed using FASTQC software and contamination and adapter removal was carried out using in-house Perl scripts.
QC’ed reads were mapped using the Bowtie 1.1.2 aligner to the Oreochromis_niloticus (Orenil1.0.cds.all) coding sequences downloaded using BioMart from Ensembl repository database.
Quantification and repetitiveness was carried using eXpress software 1.5). Total effective counts for each sample were merged; a matrix was generated using the “abundance_estimates_to_matrix.pl” Perl script included in the Trinity pipeline.
DEG analysis was performed using R Bioconductor tool edgeR through the “run_DE_analysis.pl” script from Trinity and the merged count matrix. Pairwise comparisons among each sample type (Control vs T2 or Control vs T3, each with its respective biological replicate) were performed. To determine DEG, a False Discovery Rate (FDR) of adjusted p < 0.05 was used.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Mar 09, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Aurea Orozco Rivas |
| E-mail(s) |
[email protected]
|
| Phone |
+52 44 22 38 10 68
|
| Organization name |
Instituto de Neurobiología, UNAM
|
| Department |
Neurobiología Celular y Molecular
|
| Lab |
Fisiología Evolutiva
|
| Street address |
Boulevard Juriquilla 3001
|
| City |
Querétaro |
| State/province |
Querétaro |
| ZIP/Postal code |
76230 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL23168 |
| Series (1) |
| GSE96046 |
Uncovering novel roles for thyroid hormones in teleost fishes: Differential transcriptome regulation in brain and liver by 3,5-T2 and 3’,3,5-T3 |
|
| Relations |
| BioSample |
SAMN06556235 |
| SRA |
SRX2630490 |
