NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2297728 Query DataSets for GSM2297728
Status Public on Aug 30, 2016
Title Dam-2
Sample type SRA
 
Source name adult testes
Organism Drosophila melanogaster
Characteristics genotype: yw
Sex: male
tissue: testes
developmental stage: 2 days old
Growth protocol The flies were kept at 23°C
Extracted molecule genomic DNA
Extraction protocol 25 adult testes were dissected in PBS.
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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
 
Description control sample
Data processing Sequenced reads were trimmed for adaptor sequence using cutadapt v1.7
The reads obtained were mapped to BDGP R6 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 R6/dm6
 
Submission date Aug 29, 2016
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 (1)
GSE86205 Tissue-specific DamID profiling of chromatin proteins in Drosophila melanogaster
Relations
BioSample SAMN05714746
SRA SRX2065446

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap