|
| Status |
Public on Oct 25, 2017 |
| Title |
Wild type 2 hpf replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Whole embryos (n=40)
|
| Organism |
Danio rerio |
| Characteristics |
developmental stage: 2 hpf
genotype: wild type
tissue: whole embryo
|
| Growth protocol |
Embryos were grown at 28.5C until point of collection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol protocol
Libraries were constructed using Illumina TruSeq RNA Library Prep Kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file: 2hr_gene_exp.diff
|
| Data processing |
Reads were aligned for each sample using TopHat v2.0.13 (Trapnell et al., 2009) with the following command “tophat -o <output directory> -p 16 --no-novel-juncs -G <gene table> <Bowtie2 genome index> <fastq reads>”
Transcript abundance and differential expression were determined using Cufflinks v2.2.1 (Trapnell et al., 2012) with the following command for each developmental stage “cuffdiff -p 16 -b <genome.fa -u -L <labels> -o <output directory> <gene table> <wild type aligned reads .bam file> <mutant aligned reads .bam file>”
Genome_build: zv9
Supplementary_files_format_and_content: tab delimited text files containing FPKMs from cuffdiff output
|
| |
|
| Submission date |
Oct 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
James A Gagnon |
| E-mail(s) |
james.gagnon@gmail.com
|
| Organization name |
University of Utah
|
| Department |
Biological Sciences
|
| Street address |
1390 Presidents Circle, Crocker Science Center Receiving, Crocker Science Center Receiving
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL18413 |
| Series (1) |
| GSE89245 |
RNAseq of wild type and maternal-zygotic Nanog mutant (MZnanog) zebrafish embryos |
|
| Relations |
| BioSample |
SAMN05948510 |
| SRA |
SRX2273772 |
