|
| Status |
Public on Oct 23, 2023 |
| Title |
DMSO_H3K9me3_CUTTag_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryos
|
| Organism |
Danio rerio |
| Characteristics |
tissue: whole embryos
developmental stage: 6hour post fertilization
genotype: wild type
treatment: DMSO
|
| 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 100uM 5Aza-dC (treatment starts from 1-cell stage), 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 |
genomic DNA |
| Extraction protocol |
Around 100,000 cells from 6hpf embryos were used for CUT&Tag and library construction according to standard methods. Polyclonal H3K9me3 antibody from Active Motif (Cat. 39062) was used.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw sequencing reads were processed with Cutadapt (v2.7) to remove adapters
Then sequencing reads were aligned to zebrafish genome (GRCz11) using Bowtie2(v2.2.5), and then PCR duplicates were marked and removed using Picard MarkDuplicates(v2.5.0)
Read count normalized genome browser tracks were generated using bamCoverage from merged Sam files of triplicates with the following parameters: --normalizeUsing RPKM --binSize 10
Assembly: Zv11
Supplementary files format and content: bigWig files, RPKM normalized genome browser track
Library strategy: CUT&Tag
|
| |
|
| Submission date |
Dec 08, 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 |
| GSE220555 |
Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression [CUT&Tag] |
|
| Relations |
| BioSample |
SAMN32116172 |
| SRA |
SRX18541363 |
