|
Status |
Public on Mar 30, 2017 |
Title |
DamPc_aly_Rep1 |
Sample type |
SRA |
|
|
Source name |
DamPc_aly
|
Organism |
Drosophila melanogaster |
Characteristics |
strain: yw gender: male age: 3 days old tissue: adult testes
|
Growth protocol |
The flies were kept at 23°C
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Testes were collected from 3day-old males. For each biological replicate, 50 pairs of testes were used. Standard phenol-chloroform extraction method was used to isolate genomic DNA from the collected material. 0.5-1 ug DNA was used in each DamID experiment. 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. One microgram of genomic DNA was processed for library preparation using the DNA TruSeq kit. The libraries were sequenced on the Illumina MiSeq system.
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|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina MiSeq |
|
|
Description |
DamPc/aly-mutant testes Pc_aly_Testes_track.wig.gz
|
Data processing |
Library strategy: DamID Sequenced reads were trimmed for adaptor sequence using cutadapt v1.7 The reads obtained were mapped to BDGP R5 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
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|
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Submission date |
Mar 29, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Petr Laktionov |
E-mail(s) |
laktionov@mcb.nsc.ru
|
Organization name |
Institute of molecular and cellular biology SD RAS
|
Lab |
Genomics lab
|
Street address |
Lavrenitev ave 8/2
|
City |
Novosibirsk |
ZIP/Postal code |
630090 |
Country |
Russia |
|
|
Platform ID |
GPL16479 |
Series (2) |
GSE97176 |
Genome-wide profiling of gene expression and transcription factors binding reveals new insights into the mechanisms of gene regulation during Drosophila spermatogenesis [DamID] |
GSE97182 |
Genome-wide profiling of gene expression and transcription factors binding reveals new insights into the mechanisms of gene regulation during Drosophila spermatogenesis |
|
Relations |
BioSample |
SAMN06651205 |
SRA |
SRX2683499 |