|
| Status |
Public on Aug 25, 2017 |
| Title |
tet2-/-;tet3-/- mutants at 36hpf |
| Sample type |
SRA |
| |
|
| Source name |
whole eye tissue
|
| Organism |
Danio rerio |
| Characteristics |
strain: TL
genotype/variation: tet2-/-;tet3-/- mutants
tissue: dissected eyes
age: 36 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 NextSeq 500 |
| |
|
| Description |
processed data file: Tet23_36hpf_GE_all.xlsx
|
| Data processing |
base-calling, demultiplexing done at University of Pittsburgh Genomic Research Core
fastq files quality checked using FastQC
mapped using CLC Genomics Grid Worker 7.5.1
gene counting and differentially expressed genes identified using CLC Genomics Grid Worker 7.5.1
Genome_build: GRCz10
Supplementary_files_format_and_content: Tet23_36hpf_GE_all.xlsx
|
| |
|
| Submission date |
Mar 30, 2017 |
| 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 |
GPL20828 |
| Series (1) |
| GSE80134 |
Tet-mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell-extrinsic signaling pathways |
|
| Relations |
| BioSample |
SAMN06667677 |
| SRA |
SRX2692998 |
