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| Status |
Public on Jul 18, 2016 |
| Title |
EyeDisc_K27me3 |
| Sample type |
SRA |
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| Source name |
Eye discs
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| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: L3
antibody: K27me3
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
crosslinking was performed for 15 min in the presence of 1.8% formaldehyde during tissue homogenization. Chromatin extracts of embryos were sonicated using a Bioruptor (Diagenode) for 15 min (settings 30 sec on, 30 sec off, high power).
To obtain the recommended quantity of DNA several Ips were prepared, pooled and resuspended in a volume of 20ml (12 to 14 Ips for Pc or Ph, 3 to 4 Ips for H3K27me3 and 3 Ips for H3K27ac). Sample preparation was done with Illumina kit (ref. IP-102-1001) following manufacturer’s instructions.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
rep1 and rep2
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| Data processing |
filtering with CASAVA 1.8.2 from Illumina
Alignment with CASAVA 1.8.2 from Illumina
For PC, PH, K27Ac : Peak calling with MACS 1,3,7, genome at 120Mb, tag size at 36bp, other parameters as standards parameters. Only the peaks wth FDR<=10 % and fold-enrichment>=2 have been kept
For K27me3 : Domain analysis with SICER 1,1 with input as control library, a redundancy threshold of 4, a window size of 500bp, an effective genome fraction of 0.7, a gap size of 2kb and a threshold of 10 %. To define highly confident targets, the 500bp windows with 2 fold enrichment have been considered.
Genome_build: Dm 3
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| Submission date |
Oct 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Giacomo Cavalli |
| E-mail(s) |
[email protected]
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| Organization name |
CNRS
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| Lab |
INSTITUTE of HUMAN GENETICS
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| Street address |
IGH - CNRS, 141, rue de la Cardonille
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| City |
Montpellier |
| ZIP/Postal code |
34396 Cedex5 |
| Country |
France |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE74080 |
Massive redeployment of PRC1 proteins suppresses tumor formation during Drosophila development |
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| Relations |
| BioSample |
SAMN04192198 |
| SRA |
SRX1342243 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1910623_EyeDisc_K27me3_domains.bed.gz |
2.6 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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