GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1647362 Query DataSets for GSM1647362
Status Public on Jun 12, 2015
Title Dm_Rpb3_X_ChIP_(20140917_3)
Sample type SRA
Source name Crosslinked MNase digested chromatin
Organism Drosophila melanogaster
Characteristics cell line: Drosophila S2 cells
antibody: Rpb3 (PMID: 15629721)
Extracted molecule genomic DNA
Extraction protocol Drosophila S2 cells were crosslinked using formaldehyde for 10 minutes at room temperature. Chromatin was fragmented using MNase and then sonicated to ensure complete extraction of chromatin and associated proteins. Chromatin was immunoprecipitated using an antibody against Rpb3. DNA was extracted from the immunoprecipitated chromatin and subjected to Illumina (Solexa) sequencing.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Description Total RNA Polymerase II chromatin immunoprecipitations was performed in Drosophila S2 cells using an antibody against Rpb3.
library strategy: Modified ChIP-seq (see PMID 22025700)
Data processing 1. We used Novoalign (v2.08.03) with options "-F STDFQ -a -r Random" to map paired-end 25bp reads to release 5.51 of the D.melanogaster genomic sequence obtained from FlyBase. 2. We extracted properly paired reads (Supplementary file .bed). 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig)
Submission date Mar 31, 2015
Last update date May 15, 2019
Contact name Jorja Henikoff
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
Platform ID GPL17275
Series (1)
GSE67454 A simple method for generating high-resolution maps of genome wide protein binding
BioSample SAMN03453193
SRA SRX974394

Supplementary file Size Download File type/resource
GSM1647362_Dm_Rpb3_X_ChIP.bed.gz 81.1 Mb (ftp)(http) BED
GSM1647362_Dm_Rpb3_X_ChIP.wig.gz 106.4 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap