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| Status |
Public on Jul 22, 2024 |
| Title |
4.5 hpf embryo, IgG |
| Sample type |
SRA |
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| Source name |
embryo
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| Organism |
Danio rerio |
| Characteristics |
timepoint: 4.5hpf
genotype: AB
antibody: IgG
tissue: embryo
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| 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
E coli DNA spike in
mIgG.bw (CUTnRUN_conf_exps)
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| 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
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| Submission date |
Feb 21, 2024 |
| Last update date |
Jul 22, 2024 |
| Contact name |
Mary Goll |
| E-mail(s) |
mary.goll@uga.edu
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| Organization name |
University of
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| Department |
Genetics
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| Street address |
130 East Green Street
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| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
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| Platform ID |
GPL20828 |
| Series (1) |
| GSE256288 |
Uncoupled H3K9me3 nucleation and reinforcement during early zebrafish embryogenesis |
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| Relations |
| BioSample |
SAMN40024185 |
| SRA |
SRX23689047 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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