|
| Status |
Public on Sep 15, 2009 |
| Title |
H3K27me3_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Xenopus tropicalis |
| Characteristics |
developmental stage: 11-12 embryo
antibody: H3K27me3
|
| Growth protocol |
Xenopus tropicalis embryos were obtained from a natural mating procedure after human chorion gonadotropin injection, dejellied in 2% cysteine and collected at the indicated stage.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin (300-600 embryos) was fixed in 1% formaldehyde, sheared using a Branson sonifier, immunoprecipitated using 1-5 µg of antibody, washed, decrosslinked, DNA was purified and sequenced using a Illumina Genome Analyzer according to the manufacturer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against H3K27me3
Processed_data_file: H3K27me3.bed
Processed_data_file: H3K27me3_enriched.bed
Raw data file: 202KJAAXX_1_sequence.fastq
Raw data file: 204BGAAXX_6_sequence.fastq
Raw data file: 204BGAAXX_8_sequence.fastq
Raw data file: 204BGAAXX_5_sequence.fastq
Raw data file: 204BGAAXX_7_sequence.fastq
Raw file type: fastq
|
| Data processing |
32 bp reads were aligned to the JGI Xenopus tropicalis genome assembly (version 4.1) and filtered for uniqueness. Enriched regions for H3K4me3 and H3K27me3 were determined by a sliding window approach of 500bp using a threshold of threshold (determined by a FDR approach) of 9 and 12 reads for H3K4me3 and H3K27me3, respectively.
|
| |
|
| Submission date |
Dec 17, 2008 |
| Last update date |
May 15, 2019 |
| Contact name |
Gert Jan Veenstra |
| E-mail(s) |
g.veenstra@science.ru.nl
|
| Phone |
+31 24 3610541
|
| Organization name |
Radboud University
|
| Department |
Molecular Developmental Biology
|
| Street address |
Geert Grooteplein 28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL9405 |
| Series (1) |
| GSE14025 |
A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos |
|
| Relations |
| SRA |
SRX012331 |
| BioSample |
SAMN00004607 |
