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Sample GSM2492002 Query DataSets for GSM2492002
Status Public on Mar 30, 2017
Title Nup98-2
Sample type SRA
 
Source name brains
Organism Drosophila melanogaster
Characteristics developmental stage: 3rd instar larva
tissue: brains
chip antibody: Nup98 (Capelson et al., (2010))
genotype/variation: wild type
Extracted molecule genomic DNA
Extraction protocol Lysates from embryonic cells or 3rd instar brains were clarified from sonicated nuclei and histone-DNA or Nup-DNA complexes were isolated with specific antibody
Libraries were prepared according to Illumina's instructions for NextSeq® 500/550 High Output Kit v2 (FC-404-2005).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Raw fastq files were trimmed to remove low quality base calls using Trimmomatic, with parameter "LEADING:3 TRAILING:3 SLIDINGWINDOW:3:3 MINLEN:30".
Trimmed reads were aligned to dm3 using Bowtie2, allowing for only uniquely aligned reads (MAPQ > 10) to be reported.
Duplicate reads and mitochondria reads were removed using Samtools and Bedtools.
Significant peaks were called using MACS2, with parameter "--qvalue 0.05 -m 2 50".
Bedgraphs were generated using the command "bedtools genomecov", library sizes were normalized to 10 million reads per sample.
BigWig files were then converted from bedgraph files using command "bedGraphToBigWig".
Genome_build: dm3
Supplementary_files_format_and_content: bigwig files were converted from bedgraph files, which were generated using Bedtools. Scores were normalized to 10 million reads per sample.
 
Submission date Feb 15, 2017
Last update date May 15, 2019
Contact name Yemin Lan
Organization name University of Pennsylvania
Street address 3400 Civic Center Blvd
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL19132
Series (1)
GSE94922 Nuclear Pores provide a scaffold for induced enhancer promoter contacts
Relations
BioSample SAMN06336848
SRA SRX2564149

Supplementary file Size Download File type/resource
GSM2492002_Nup98-2.norm.bigWig 105.2 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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