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Sample GSM2553064 Query DataSets for GSM2553064
Status Public on Mar 30, 2017
Title Dam_Rep1_CG9879_Control
Sample type SRA
 
Source name Dam_CG9879_Control
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.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
 
Description CG9879 DamID control sample
CG9879_WT_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
 
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 SAMN06651194
SRA SRX2683481

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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