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Sample GSM1461744 Query DataSets for GSM1461744
Status Public on Apr 12, 2016
Title Input ChIP-seq WT
Sample type SRA
 
Source name 3rd instar larvae wing discs
Organism Drosophila melanogaster
Characteristics genotype/variation: Act5c-Gal4 (WT)
genotype/variation: y1 w*; P{Act5C-GAL4}25FO1/CyO, y+
tissue: 3rd instar larvae wing discs
Treatment protocol Act5c-Gal4 virgins are crossed with Act5c-Gal4 or indicated RNAi (yw; UAS-dsRNA Polycomb, PR-Set7 or E(z)) males under standard conditions at 25 degrees
Growth protocol Drosophila larvae are grown under standard conditions at 25 degrees.
Extracted molecule genomic DNA
Extraction protocol For RNA-seq, drosophila third instar larvae wing discs from indicated genetypes were dissected into Trizol, and total RNA was extracted for the construction of sequencing libraries. For ChIP-seq, drosophila third instar larvae wing discs from Act5c-Gal4 were cross-linked, sonicated and subjected for ChIP assay with anti-H4K20me1 antibody. After reverse cross-link and protein digestion with proteinase K, the immunoprecipitated genomic DNA was extracted with DNA purification kit (QIAGEN) and for construction of sequencing libraries.
ChIP-seq and unstrand RNA-seq libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Basecalling was performed using CASAVA version 1.4
ChIP-seq reads were mapped to dm3 using bowtie version 1.0.0 with at most 2-mismatches allowed. Only uniquely mapped reads were kept for further analysis.
H4K20me1 peaks were called using SICER with window size 200bp, gap size 200bp, E value 0.01, fragment length 150bp, redundant reads level 3.
Mapped redundant-removed reads were extended to 200bp and then converted into total reads number normalized bigWig format.
RNA-seq reads were first mapped to dm3 refSeq transcriptome and then unmapped reads were mapped to dm3 reference using TopHat version 2.0.11 with at most 2-mismatches allowed and multiple mapped cutoff 5.
Genes expression level were quantified using cufflinks. Differentially expressed genes were identified using DEGseq with P value 0.001.
Genome_build: dm3
Supplementary_files_format_and_content: Peak files in BED format. BigWig files for ChIP-seq datasets were generated using UCSC genome browser tools. Genes expression level for each sample in table file.
 
Submission date Jul 30, 2014
Last update date May 15, 2019
Contact name Gang Wei
E-mail(s) weigang@picb.ac.cn
Organization name CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Lab Key Laboratory of Computational Biology
Street address 320 Yue Yang Road
City Shanghai
State/province Shanghai
ZIP/Postal code 200031
Country China
 
Platform ID GPL13304
Series (1)
GSE59924 A Novel Role of Polycomb in Positive Transcription Regulation by Modulating H4K20me1
Relations
BioSample SAMN02947296
SRA SRX666357

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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