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Sample GSM2537266 Query DataSets for GSM2537266
Status Public on Jun 04, 2018
Title 30d_esc_E(z)_ChIPSeq_input_rep1
Sample type SRA
Source name fly muscle
Organism Drosophila melanogaster
Characteristics tissue: muscle
age: 30 day
genotype: esc289; E(z)239
Treatment protocol Fly muscles were harvested at the given age.
Growth protocol Flies were cultured in standard media at 25ºC with 60% humidity unless otherwise specified. The control (WT) line used was 5905 (FlyBase ID FBst0005905, w1118). The given genotype male flies were collected at the day of eclosion and transferred to new vials every other day during aging process.
Extracted molecule genomic DNA
Extraction protocol For ChIP-Seq, 5% mouse epigenome was used as internal control for H3K27me3 IP.
For RNA-Seq, RNA was isolated by TRIZol reagent, and polyA tail RNAs were selected.
For small RNA-seq, ~20-29 nt small RNA was recoveried by 15% TBE-UREA PAGE gels.
ChIP libraries were prepared according to instructions of NEB DNA library prep kit (NEB, E7370L). RNA libraries were prepared according to instructions of NEB Ultra RNA library prep kit (NEB, E7530L). Small RNA libraries were prepared by NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, E7300S).
ChIP-Seq or RNA-Seq or miRNA-seq
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
Data processing For ChIP-Seq, Sequencing reads were mapped to reference genome dm6 or mm10 respectively with Bowtie2 by default parameter. The peak regions were identified by homer function findPeaks with parameter –style histone -F 2 -size 3000 -minDist 5000. The overlapped peaks of replicate data-sets were found using homer function mergePeaks by default parameter. Bedtools were used to compare the peaks between different genotypes and aging stages. To get inter-peak regions, we used Bedtools to subtracted the peak regions from whole genome.
For quantitative comparison, the dm6 mapped reads were normalized to a scale factor using deeptools function bamCoverage with 10 bp bin size. The scale factor for each sample was calculated as reported (David A. Orlando et al., 2014) with a small modification. The percentage of mouse genome in input was set to the mm10 mapped reads in total mapping reads, rather than a constant. The ChIP intensity of each genes or regions were calculated using the Bwtool function bwtool summary.
For RNA-Seq comparison, Sequencing reads were mapped to dm6 with STAR by default parameter. The read counts for each genes were calculated by HTSeq-count. The count files were used as input to DESeq for differential expression analysis.
For small RNA-Seq, adapters were removed by fastx, microRNAs were identified by miRDeep2.
Genome_build: dm6 and mm10
Supplementary_files_format_and_content: bigwig files were generated by deeptools. DESeq was used for calling differential expression.
Submission date Mar 15, 2017
Last update date May 15, 2019
Contact name Hui Wang
Organization name Chinese Academy of Science
Street address Qiuyue Road 26
City Shanghai
ZIP/Postal code 200032
Country China
Platform ID GPL16479
Series (1)
GSE96654 Epigenetic Drift of H3K27me3 in Aging Links Glycolysis to Healthy Longevity
BioSample SAMN06604181
SRA SRX2642399

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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