|
| Status |
Public on May 08, 2019 |
| Title |
sibslivr1: 5 dpf Livers non transgenic siblings-1 |
| Sample type |
SRA |
| |
|
| Source name |
liver/pooled
|
| Organism |
Danio rerio |
| Characteristics |
tissue: pooled liver
genotype/variation: WT
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tg(fabp10:nAtf6-cherry; cmlc2:GFP)C+/, were outcrossed to WT TAB 14 and the embryos were sorted and segregated basing on the expression of Cmlc2:GFP. The three different clutches of embryos were collected and dissected over three different days. The embryos were collected inbetween 10- 11 AM. The Liver dissection was also performed on the 5dpf larvae before noon. 25 livers from 5dpf embryos were pooled per sample( Transgenic and WT siblings in two different tubes) and RNA extracted with Trizol as per manufacturer's instructions.The RNA was later treated with DNAse to remove any DNA. They RNA concentration was taken on the Q bit, and then analysed on the Bioanalyser for the integrety and quality of RNA. The RIN score for the samples was above 8.5
RNA-seq libraries were prepared according to Illumina TruSeq RNA sample preparation version 2 protocol with Ribo-Zero Gold (Catalog #: RS-122-2501)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
The raw reads were quality assessed using FastQC v0.11.5. The raw reads were then quality trimmed using Trimmomatic,trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36
Alignments of trimmed reads were performed using tophat2 v2.1.0, with the parameters “–no-novel-junctions” and “–G”
Accepted bam files were used for counting gene read numbers with HTSeq, -a 10 -s no
Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor
Genome_build: GRCz10
Supplementary_files_format_and_content: .txt Reads count of genes
|
| |
|
| Submission date |
May 07, 2019 |
| Last update date |
Sep 01, 2021 |
| Contact name |
Kirsten Sadler Edepli |
| E-mail(s) |
kirsten.edepli@nyu.edu
|
| Phone |
971568327587
|
| Organization name |
New York University Abu Dhabi
|
| Department |
Biology
|
| Street address |
PO Box 129188
|
| City |
Abu Dhabi |
| State/province |
Abu Dhabi |
| ZIP/Postal code |
000 |
| Country |
United Arab Emirates |
| |
|
| Platform ID |
GPL18413 |
| Series (2) |
| GSE130800 |
Transcriptomic profiling of zebrafish livers with nAtf6 overexpression at collected at 78 and 120 hpf |
| GSE130801 |
Transcriptomic profiling of zebrafish livers at 5 dpf with nAtf6 overexpression or in response to ethanol exposures |
|
| Relations |
| BioSample |
SAMN11585748 |
| SRA |
SRX5800871 |
