|
| Status |
Public on Nov 27, 2018 |
| Title |
WT2A |
| Sample type |
SRA |
| |
|
| Source name |
Fin
|
| Organism |
Danio rerio |
| Characteristics |
development stage: Larvae
genotype/variation: WT
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using Trizol (Invitrogen) and precipitated with isopropanol.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit), with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run, using the TruSeq SBS v4 Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
counts_scaled_DESeq.txt.gz
|
| Data processing |
Reads were mapped to the Zebrafish genome (danRer7) using the rnaStar aligner v2.5.0a. We used the 2 pass mapping method outlined in Engström et.al (Nat. Meth. 2013). The first mapping pass used a list of known annotated junctions from Ensemble. Novel junctions found in the first pass were then added to the known junctions and a second mapping pass was done (on the second pass the RemoveNoncanoncial flag was used). Expression counts were computed from the mapped reads using HTSeq v0.5.3 and Ensemble D.rerio v79 gene annotations. Normalization and differential expression was performed using DESeq.
Genome_build: danRer7
Supplementary_files_format_and_content: Tab-delimited normalized RNA-seq counts per million for each sample.
|
| |
|
| Submission date |
Jun 27, 2018 |
| Last update date |
Nov 27, 2018 |
| Contact name |
John R. Edwards |
| E-mail(s) |
jredwards@wustl.edu
|
| Organization name |
Washington University School of Medicine
|
| Department |
Center for Pharmacogenomics
|
| Street address |
660 S. Euclid Ave, Campus Box 8220
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL18413 |
| Series (2) |
| GSE116358 |
Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [ssRNA-seq] |
| GSE116360 |
Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome |
|
| Relations |
| BioSample |
SAMN09503554 |
| SRA |
SRX4314653 |
