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| Status |
Public on Jan 10, 2016 |
| Title |
Dam-Pc-SG-SuUR_KO-2 |
| Sample type |
SRA |
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| Source name |
salivary glands
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| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: SuUR mutant
developmental stage: L3
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| Growth protocol |
The flies were kept at 23°C
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
50 salivary glands were dissected accurately - fat body was removed completely.
DNA was isolated using phenol-chloroform method. 1ug of genomic DNA was digested by DpnI endonuclease. Digested DNA was ligated with double-stranded DNA adapters and then digested with DpnII endonuclease. Next, methylated fragments were selectively amplified using adapter-specific primer. Before the preparation of libraries for Illumina DamID-seq, the adapters used in DamID procedure were cut with DpnII enzyme. No further fragmentation was performed.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Library strategy: DamID-seq
Sequenced reads were trimmed for adaptor sequence using cutadapt v1.7
The reads obtained were mapped to BDGP R5/dm3 Drosophila genome assembly using MOSAIK software with following parameters: -m all -mmp 0.1 -act 20 -a single
For further analysis, only the reads that started with GATC sequence were retained. The number of reads for each genomic fragment between the neighboring GATC sites (GATC fragments) was summed up.
The data were filtered for reproducibility: all GATC fragments were sorted according to the total read count in two biological samples. This list was binned into groups of 200 fragments having similar read counts. For each GATC fragment, a difference in read counts was calculated between the replicates. Those fragments that showed the difference above 2 standard deviations in the particular group were filtered out.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: wig files containing scores for each GATC fragment of the genome. Score represents -Log10(P), where P is significance level assessed with exact Fisher’s test for each GATC region in the genome. Positive values were ascribed to GATC fragments enriched in Dam-X sample, while negative values to those enriched in Dam-alone sample.
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| Submission date |
Nov 11, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniil Maksimov |
| E-mail(s) |
vift@mail.ru
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| Organization name |
MCB NSC RAS
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| Lab |
Genomics lab
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| Street address |
Lavrentjeva ave., 8/2
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| City |
Novosibirsk |
| ZIP/Postal code |
630090 |
| Country |
Russia |
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| Platform ID |
GPL16479 |
| Series (2) |
| GSE74907 |
Examination of SUUR and Pc chromatin proteins in slivary glands in presence or absence of SuUR mutation using DamID technique |
| GSE74909 |
Repressive Histone Marks Renewal Impedes Replication Fork Progression and Contributes To Late Replication in Drosophila |
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| Relations |
| BioSample |
SAMN04260119 |
| SRA |
SRX1426942 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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