|
| Status |
Public on Aug 25, 2017 |
| Title |
sibling at 72hpf |
| Sample type |
SRA |
| |
|
| Source name |
whole eye tissue
|
| Organism |
Danio rerio |
| Characteristics |
strain: TL
genotype/variation: sibling control
tissue: dissected eyes
age: 72 hour-postfertilization
|
| Treatment protocol |
none
|
| Growth protocol |
zebrafish embryos raised under standard condition
|
| Extracted molecule |
total RNA |
| Extraction protocol |
whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol
RNA samples were processed for RNAseq using Ambion poly-A capture kit and NEB Next kit for cDNA synthesis and library prep.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
base-calling, demultiplexing done at the Genome Sequenicng and Analysis Facility, UT Austin
fastq files quality checked using FastQC
mapped using TopHat with annotated spliced junction
gene counting and differentially expressed genes identified using Tuxedo Suite (Trapnell et al., 2012)
Genome_build: GRCz10
|
| |
|
| Submission date |
Apr 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jeffrey M Gross |
| Organization name |
University of Pittsburgh
|
| Department |
Ophthalmology
|
| Lab |
Gross
|
| Street address |
3501 Fifth Avenue
|
| City |
Pittsburgh |
| State/province |
Pennsylvania |
| ZIP/Postal code |
15217 |
| Country |
USA |
| |
|
| Platform ID |
GPL18413 |
| Series (1) |
| GSE80134 |
Tet-mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell-extrinsic signaling pathways |
|
| Relations |
| BioSample |
SAMN04632347 |
| SRA |
SRX1689713 |
