|
| Status |
Public on Oct 23, 2023 |
| Title |
WT_5AzadC_12hpf_totalRNA_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
zebrafish embryos
|
| Organism |
Danio rerio |
| Characteristics |
developmental stage: 12hour post fertilization
genotype: wild type
treatment: 5AzadC
|
| Treatment protocol |
Newly fertilized eggs were collected immediately after spawning, and placed around 50 per well in a 6 well plate. Embryos were treated with 5 mL 100uM 5Aza-dC , or with 0.1% DMSO for control group.
|
| Growth protocol |
Adult wild type AB/Tuebingen zebrafish were maintained on a 14h:10h light:dark cycle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Treated embryos were collected in Trizol at 12hpf, and grinded with motar and pestle. Total RNA was extracted with phenol:chloroform:isoamyl alcohol, then aqueous layer were purified with Zymo Direct-zol RNA Miniprep kit.
Total RNA-seq libraries were constructed.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequencing reads were mapped with STAR with default setting (v2.7.2a)
Count tables were generated by featureCounts (v2.0.3 in subread) using GRCz11.102.gtf with paired-end mode.
Differentially expressed genes were identified using DESeq2 (v1.22.2 in R/3.5.1)
Read count normalized genome browser tracks were generated using bamCoverage from merged Sam files of triplicates with the following parameters: --normalizeUsing RPKM --binSize 10
Genome_build: Zv11
Supplementary_files_format_and_content: bigWig files and txt files
|
| |
|
| Submission date |
Feb 21, 2022 |
| Last update date |
Oct 23, 2023 |
| Contact name |
Fanju Meng |
| E-mail(s) |
fanju_meng@urmc.rochester.edu
|
| Organization name |
University of Rochester Medical Center
|
| Department |
Biomedical Genetics
|
| Street address |
601 Elmwood Avenue
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
| |
|
| Platform ID |
GPL21741 |
| Series (2) |
| GSE162207 |
Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression |
| GSE197131 |
Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression |
|
| Relations |
| BioSample |
SAMN26137883 |
| SRA |
SRX14241855 |
