|
| Status |
Public on Dec 15, 2015 |
| Title |
H3K36me3_stage12 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Xenopus tropicalis |
| Characteristics |
developmental stage (nf): NF12
treatment: not injected
chip antibody: anti-H3K36me3 (Abcam ab9050)
|
| Treatment protocol |
Fertilised eggs were injected with 2,3 nl of 2,67 ng/ul α-amanitin and developed until the control embryos reached mid-gastrulation (stage 11)
|
| Growth protocol |
Embryos were obtained by in vitro fertilisation and grown at 22 celcius untill the approptate developmental stage.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Protein-DNA complexes were isolated with antibody from whole embryo lysates that were fixed, sonicated and yolk depleted.
Libraries were prepared with the Kapa Hyper Prep kit (Kapa Biosystems), and sequencing was done on the Illumina HiSeq2000 platform.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Three independent biological replicates were pooled.
|
| Data processing |
Reads were mapped to the reference Xenopus tropicalis genome JGI7.1, using the BWA allowing one mismatch
We used MACS2 with standard settings and q-value of 0.05. Fragment size was determined using phantompeakqualtools . Broad settings (--BROAD) were used for H3K4me1, H3K36me3, H3K27me3, H3K9me2, H3K9me3, H4K20me3 and RNAPII. Broad and narrow peaks were merged for H3K4me3. For H3K9ac narrow peaks were used
Peaks that showed at least 75% overlap with 1 kb regions that have <65 input reads, and peaks that have a ChIP-seq RPKM > 95 percentile of random background regions are excluded from further analysis.
Only scaffolds 1-10 were included in the analysis. Relative RPKM was calculated by dividing the ChIP-seq RPKM of the peaks by the ChIP-seq RPKM of 95 percentile of random background regions.
Relative RPKM was calculated by dividing the ChIP-seq RPKM of the peaks by the ChIP-seq RPKM of 95 percentile of random background regions.
Genome_build: JGI7.1
Supplementary_files_format_and_content: wig files were generated using bam2bw (https://bitbucket.org/simonvh/bam2bw/src); Scores are scaled with scaling factor 1000000/[total #reads]
Supplementary_files_format_and_content: bed files contain peak locations (scaffold, start, stop)
|
| |
|
| Submission date |
Apr 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Saartje Hontelez |
| E-mail(s) |
s.hontelez@ncmls.ru.nl
|
| Organization name |
Radboud University
|
| Department |
Molecular developmental biology
|
| Street address |
Geert Grooteplein 28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL15472 |
| Series (1) |
| GSE67974 |
Embryonic transcription is controlled by maternally defined chromatin state |
|
| Relations |
| BioSample |
SAMN03491020 |
| SRA |
SRX999345 |
