|
| Status |
Public on Jul 22, 2024 |
| Title |
2.5 hpf embryo, IgG, rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Danio rerio |
| Characteristics |
timepoint: 2.5hpf
genotype: AB
antibody: IgG
tissue: embryo
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
This is H3K9me3 CUT&RUN data isolated from zebrafish embryos. Genomic DNA libraries were prepared using an illumina protocol.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
E coli DNA spike in
mIgG.bw (CUTnRUN_timecourse)
|
| Data processing |
Short reads (<20 bp) and adaptor sequences were removed using TrimGalore
Trimmed reads were aligned to the zebrafish genome assembly (GRCz.11 Ensemble release 98) using STAR with the following paramters: --readFilesCommand zcat –outSAMtype BAM SortedByCoordinate –outSAMmultNmax 1 –alignEndsType EndToEnd –alignIntronMax 1 –alignMatesGapMax 2000
Alignments were then filtered using SAMtools for a MAPQ score of 1 and PCR duplicates were removed using Picard MarkDuplicates
data was then normalized for library size and DNA spike-in using BEDtools “genomecov”
The Hypergeometric Optimization of Motif EnRichment (HOMER) software package was used to identify peaks over IgG using the following parameters: -style histone -minDist 1000 -gsize 1.5e9 -F 4
replicates were then analyzed using ChIPr with parameter -m 2 to identify reproducible peaks
Assembly: GRCz.11 release 98
Supplementary files format and content: bigwigs, averaged bigwigs, and peak files
Library strategy: CUT&RUN
|
| |
|
| Submission date |
Feb 21, 2024 |
| Last update date |
Jul 22, 2024 |
| Contact name |
Mary Goll |
| E-mail(s) |
mary.goll@uga.edu
|
| Organization name |
University of
|
| Department |
Genetics
|
| Street address |
130 East Green Street
|
| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
| |
|
| Platform ID |
GPL20828 |
| Series (1) |
| GSE256288 |
Uncoupled H3K9me3 nucleation and reinforcement during early zebrafish embryogenesis |
|
| Relations |
| BioSample |
SAMN40024212 |
| SRA |
SRX23689020 |
