|
| Status |
Public on Nov 27, 2018 |
| Title |
ifih1Mu_z24WT_3 |
| Sample type |
SRA |
| |
|
| Source name |
Fin
|
| Organism |
Danio rerio |
| Characteristics |
development stage: Larvae
genotype/variation: ifih1 Mutant
tag: zbtb24 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 |
ifih1_z24DM.genes.fpkm_table.txt.gz
|
| Data processing |
Raw RNA-seq FASTQ reads were trimmed for adapters and preprocessed to remove low-quality reads using Trimmomatic v0.33 (arguments: LEADING:3 TRAILING:3 MINLEN:36) (Bolger et al., 2014) prior to mapping to the Danio rerio GRCz10 reference genome assembly. Reads were mapped using TopHat v2.1.1 (Kim et al., 2013) supplied with a reference General Features File (GFF) to the Danio rerioGRCz10 reference genome assembly, and with the following arguments: -i 10 -I 5000 --library-type fr-firststrand. Gene expression was estimated using Cuffquant (a tool from Cufflinks v2.2.1), with following arguments --library-type fr-firststrand. Expression level were normalized in FPKM units by Cuffnorm (a tool from Cufflinks v2.2.1), with following arguments --library-type fr-firststrand.
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited normalized RNA-seq FPKM 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) |
| GSE116359 |
Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome [dsRNA-seq] |
| GSE116360 |
Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome |
|
| Relations |
| BioSample |
SAMN09504200 |
| SRA |
SRX4314663 |
