|
| Status |
Public on Sep 19, 2013 |
| Title |
CTRL 3dpf |
| Sample type |
SRA |
| |
|
| Source name |
Whole zebrafish larvae
|
| Organism |
Danio rerio |
| Characteristics |
Stage: 3 days post fertilization
tissue: whole larvae
genetic background: AB
genotype: wild type
|
| 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 |
Larvae for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 10 ug of total RNA for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base-calls and demultiplexing using Illumina Casava 1.8.
Low-quality base-calls were removed using the 'quality_trim' application in the CLC bio Assembly Cell 3.2 software package. Settings: minimum remaining read length 30, minimum quality 20, at least 50% of the read must be good quality.
Reads were aligned to Ensembl predicted cDNAs (Danio_rerio.Zv9.63.cdna.all.fa) using the 'clc_ref_assemble_short' application in the CLC bio Assembly Cell 3.2 software package. Settings: mismatch cost 2, gap cost 3, deletion cost 3, score limit 8; random placement of repeats, up to 50 alignments per read.
Alignment files were translated into counts per transcript using the 'assembly_table' application, and summarized into genes based on Ensembl transcript/gene annotations using a custom script. Non-unique alignments were divided amongst target genes by ratio of unique reads, yielding a corrected total reads count per gene. This count was divided by the total length of constituent transcripts and by the total number of aligned read, and multiplied by a billion, to arrive at a RPKM-like expression value.
Genome_build: Zv9 (Ensembl release 63)
Supplementary_files_format_and_content: Tab-delimited text files with read counts and RPKM-normalized values for every gene.
|
| |
|
| Submission date |
Nov 01, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
marina mione |
| E-mail(s) |
maria.mione@kit.edu
|
| Organization name |
Karlsruhe Institute of Technology
|
| Department |
Institute of Toxicology and Genomics
|
| Street address |
Hermann-von-Helmholtz-Platz 1
|
| City |
Eggesteing Leopolshafen |
| ZIP/Postal code |
76344 |
| Country |
Germany |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE41988 |
Targeting oncogene expression to endothelial cells induces proliferation of the myelo-erythroid lineage by repressing the notch pathway |
|
| Relations |
| BioSample |
SAMN01797979 |
| SRA |
SRX202490 |
