|
| Status |
Public on Apr 27, 2017 |
| Title |
H3K9me3 white-embKD_3 |
| Sample type |
SRA |
| |
|
| Source name |
ovaries
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: vasa-GAL80[ts]/+;;da-GAL4/shwhite
embryonic temperature: 28°C
chip antibody: Abcam cat≠ ab8898
|
| Growth protocol |
Flies were maintained at 18°C. After appropriate cross, embryos were shifted at 28°C to induce RNAi against white or piwi proteins.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
100 dissected ovaries were crosslinked with 1.8% formaldehyde for 10 min, and the prepared chromatin was sonicated. One-third was used for immunoprecipitation by H3K9me3 antibody. After decrosslinking, DNA was extracted and used for library preparation for sequencing. The ChIP-seq experiments were performed in three biological replicates.
Library preparation and 50nt single-read sequencing were performed by Donnelly Sequencing Centre (Toronto) on an Illumina HiSeq2500.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Read mapping on D. melanogaster genome and canonical transposons: the 50bp single-end reads were mapped on the Drosophila melanogaster genome (Release 5; dm3) with BWA. DeepTools 2.0 (bamCompare) was used to extend reads to fit average fragment length (--extendReads 200), to filter PCR duplicate (--ignoreDuplicates) and keep high quality mapped reads (and uniquely mapped) (--minMappingQuality 20) to compute the H3K9me3 enrichment with a ratio of depth normalized read (--normalizeUsingRPKM) between IP and Input. The processed data files are listed below.
Genome_build: Drosophila melanogaster, release 5
Supplementary_files_format_and_content: bigWig files
|
| |
|
| Submission date |
Jun 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
SEVERINE CHAMBEYRON |
| E-mail(s) |
severine.chambeyron@igh.cnrs.fr
|
| Organization name |
CNRS
|
| Department |
Institute of Human Genetics
|
| Lab |
Non-coding RNA, epigenetics and genome stability
|
| Street address |
141, rue de la Cardonille
|
| City |
MONTPELLIER |
| ZIP/Postal code |
34396 |
| Country |
France |
| |
|
| Platform ID |
GPL17275 |
| Series (2) |
| GSE83234 |
Piwi is required during Drosophila embryogenesis to license dual-strand piRNA clusters for transposon repression in adult ovaries [ChIP-seq] |
| GSE83238 |
Piwi is required during Drosophila embryogenesis to license dual-strand piRNA clusters for transposon repression in adult ovaries |
|
| Relations |
| BioSample |
SAMN05226683 |
| SRA |
SRX1837296 |
