|
| Status |
Public on Jan 10, 2016 |
| Title |
SuUR embr input 3 |
| Sample type |
SRA |
| |
|
| Source name |
embryos
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: SuUR mutant
chip antibody: none
tissue: 0-4h embryos
|
| Growth protocol |
Flies were raised at 23°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
20 ul of 0-4h embryos were used as starting material. Abcam anti-H3K27me3 antibodies (6002) were used for chromatin immunoprecipitation. Chromatin was sheared using BioRuptor instrument (Diagenode).
DNA from precipitated material and input were used for library preparation using Illumina Nextera protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
processed data file: SUUR_AB_div_input_profile_in_10000bp_bins_1000bp_shift.wig.gz
|
| Data processing |
The reads were mapped to BDGP R5/dm3 Drosophila genome assembly using MOSAIK software with following parameters: -m all -mmp 0.1 -act 20 -a single. Paired reads were combined.
For each genomic position, the RPM (reads per million) value was calculated for ChIP sample and input sample. Log2 of the ChIP to input ratio was used as a measure of local H3K27me3 enrichment.
To build the whole genome profile, the data were smoothed using a 10kb sliding window, step 1 kb.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: wig files containing Log2 of the ChIP to input RPM ratio smoothed using a 10kb sliding window with 1000 bp step.
|
| |
|
| Submission date |
Nov 11, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniil Maksimov |
| E-mail(s) |
vift@mail.ru
|
| Organization name |
MCB NSC RAS
|
| Lab |
Genomics lab
|
| Street address |
Lavrentjeva ave., 8/2
|
| City |
Novosibirsk |
| ZIP/Postal code |
630090 |
| Country |
Russia |
| |
|
| Platform ID |
GPL16479 |
| Series (2) |
| GSE74908 |
Functional dissection of Drosophila melanogasterSUUR protein influence on H3K27me3 profile |
| GSE74909 |
Repressive Histone Marks Renewal Impedes Replication Fork Progression and Contributes To Late Replication in Drosophila |
|
| Relations |
| BioSample |
SAMN04260131 |
| SRA |
SRX1426952 |
