|
| Status |
Public on Jun 12, 2014 |
| Title |
Control PBS 4 hpi rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Whole embryo
|
| Organism |
Danio rerio |
| Characteristics |
developmental stage: 4 days post fertilization
treatment: control
time: 4 hpi
tissue: whole embryo
genetic background: ABTL
|
| Treatment protocol |
To inject PBS and Human recombinant insulin 1 nl was injected in the caudal aorta of 4dpf zebrafish embryos using a glass capillary
|
| Growth protocol |
Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base calling was done by the Illumina HCS version 2.0.12
Data analysis was performed using Genetiles software (www.genetiles.com)
Genome_build: Zv9_toplevel
Supplementary_files_format_and_content: tab-delimited text files include read values for each Sample
|
| |
|
| Submission date |
Mar 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Rubén Marín-Juez |
| Organization name |
Max Planck Institute
|
| Street address |
Ludwigstrasse 43
|
| City |
Bad Nauheim |
| ZIP/Postal code |
61231 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18413 |
| Series (1) |
| GSE55836 |
A zebrafish model for hyperinsulinemia shows that induction of insulin resistance and immune suppression is mediated by ptpn6/shp.1 |
|
| Relations |
| BioSample |
SAMN02688136 |
| SRA |
SRX485294 |
