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Sample GSM2152433 Query DataSets for GSM2152433
Status Public on Jun 30, 2016
Title ChIP-seq input from Control-KD sample2
Sample type SRA
 
Source name Control-KD OSC
Organism Drosophila melanogaster
Characteristics cell type: Ovarian Somatic Cells (OSC)
variation: RNAi EGFP
Treatment protocol Transfection of siRNAs was performed using Cell Line 96-well Nucleofector Kit SF and 96-well Shuttle Device (Lonza).
Growth protocol Cells were grown at 26 degrees on OSC medium (Fly Extract added M3 medium).
Extracted molecule genomic DNA
Extraction protocol OSC cells were fixed, lysed, and their nuclei isolated using truChIP Chromatin Shearing Kits (Covaris) according to the manufacturer’s instructions. DNA was sonicated to ~300 bases using Bioruptor (Cosmobio), then diluted with ChIP buffer. IP was performed using 3 μg of antibodies on Dynabeads-Protein G beads. Samples were reverse cross-linked, treated with RNase and Proteinase K, and DNA was extracted.
DNA fragments from the ChIP experiment were sheared to ~200 bases using Covaris S220 (Covaris), and were used for library preparation with the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s protocol.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
 
Description processed_ChIPseqIN_2.txt
Data processing Adapters were removed from the ChIP-seq reads using Cutadapt, and subsequent reads shorter than 50 nt were discarded. ChIP-seq reads were mapped to the Drosophila genome (dm3) using Bowtie 1.0.1 (Langmead et al., 2009), using --M 1 --best --strata parameters. Reads mapped to the genome were extracted and mapped to Drosophila melanogaster transposon consensus sequences from Repbase (Jurka, 1998), permitting up to three mismatches and extracting those that mapped uniquely to the transposon consensus sequence.
Genome_build: dm3
Supplementary_files_format_and_content: Normalized read counts mapped to each transposon consensus sequence (Tab delimited format, txt).
 
Submission date May 13, 2016
Last update date Jul 03, 2021
Contact name Yuka W. Iwasaki
E-mail(s) iwasaki@keio.jp
Organization name Keio University School of Medicine
Department Department of Molecular Biology
Lab Siomi Lab
Street address 35 Shinanomachi, Shinjuku-ku,
City Tokyo
ZIP/Postal code 160-8582
Country Japan
 
Platform ID GPL16479
Series (1)
GSE81434 Piwi modulates chromatin accessibility by regulating multiple factors including histone H1 to repress transposons
Relations
BioSample SAMN04999499
SRA SRX1760705

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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