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Sample GSM1061007 Query DataSets for GSM1061007
Status Public on Feb 09, 2013
Title ChIP-seq H3K9me3 nos-GAL4->piwi
Sample type SRA
 
Source name ChIP-seq H3K9me3 nos-GAL4->piwi
Organism Drosophila melanogaster
Characteristics tissue: ovaries
age: 3-5 days
chip antibody: H3K9me3 (Abcam, ab8898)
Treatment protocol ovaries were dissected on ice
Growth protocol flies were kept at 25 degrees
Extracted molecule genomic DNA
Extraction protocol ChIP-seq: chromatin from 50 ovaries was fragmented on Bioruptor during 14 min (2 cycles, 7 min each), an aliquot was kept as "input", the rest was used for ChIP with H3K9me-ab. The detailed protocols can be found in the Rozhkov et al, 2013
The detailed methods described in the Rozhkov et al. 2013
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
 
Data processing Reads were aligned to consensus drosphila transposon sequences (v9.4.1 available from flybase.org) using bowtie2 (version 2.0.0-beta7) and the following parameters: -p2 -k 10 -N1
Reads were separately aligned to the dm3 genome using bowtie2 and the same parameters
For ChIPseq libraries, peaks were identified using SICER (version 1.1) and the following parameters: redundancy threshold =1, fragment size = 250, window size = 500, gap size = 500, FDR = 0.05, effective genome size = 0.72
Genome_build: dm3
 
Submission date Jan 08, 2013
Last update date May 15, 2019
Contact name Nikolay V Rozhkov
E-mail(s) nik.rozhkov@gmail.com, rozhkov@cshl.edu
Organization name CSHL
Lab Hannon
Street address 1 Bungtown Rd.
City Cold Spring Harbor
State/province NY
ZIP/Postal code 11724
Country USA
 
Platform ID GPL16479
Series (1)
GSE43360 Multiple roles for Piwi in silencing Drosophila transposons
Relations
SRA SRX215630
BioSample SAMN01883292

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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