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Sample GSM1356189 Query DataSets for GSM1356189
Status Public on Nov 30, 2015
Title PARP-1 ChIP-seq replicate 3
Sample type SRA
 
Source name late embryonic stage cells
Organism Drosophila melanogaster
Characteristics cell type: late embryonic cells
passages: 10--15
strain: S2
antibody: PARP-1 (Active motif-39559)
Growth protocol D. Melanogaster S2-DRSC cells (obtained from the Drosophila Genomics Resource Center) were cultured in Schneider's Drosophila medium (Invitrogen) supplemented with 10% FCS (Hyclone).
Extracted molecule genomic DNA
Extraction protocol MNase digested nuclei and histone-DNA complexes were isolated with specific antibody.
Libraries were prepared according to Applied Biosystems protocol for SOLiD4 fragment paired-end sequencing. Briefly, DNA was end-repaired and 5’-phosphorylated by incubation in DNATerminator end-repair kits, as recommended by the manufacturer (Lucigen Corp., Middleton, WI). SOLiD adapters were ligated and the DNA molecules PCR amplified (very low cycle number) and sequenced by using the Applied Biosystems protocol for SOLiD fragment paired-end sequencing. After adapter ligation DNA was PCR amplified with SoLiD primers for less than 12 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on a SoLid flow cell for cluster generation.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model AB SOLiD 4 System
 
Data processing Align(by Bowtie) the reads with their original length and find the uniquely mapped reads by increasing mismatch threshold from 0 to 3
For the reads can not be mapped, we trimmed the reads to 40bp (trimmed off the color from the end), and used the first 40bp color to map the reads. Mismatch threshold is increased from 0 to 3.
For the reads can not be mapped, we further trimmed the reads to 30bp(kept the first 30bp color of the reads), the mismatch threshold is from 0 to 2.
The alignment results from above steps were combined.
Genome_build: dm3
Supplementary_files_format_and_content: tab delimited text files containing combined reads count of uniquely mapped fragment at each genomic position
 
Submission date Mar 24, 2014
Last update date May 15, 2019
Contact name Yvonne Nsokika Fondufe-Mittendorf
E-mail(s) y.fondufe-mittendorf@uky.edu
Phone 8593230091
Organization name University of Kentucky
Department Biochemistry
Lab Mittendorf
Street address 741 South Limestone dr.
City Lexington
State/province KY
ZIP/Postal code 40536-0509
Country USA
 
Platform ID GPL14601
Series (1)
GSE56120 Genome-wide maps of PARP-1-bound nucleosomes.
Relations
BioSample SAMN02697227
SRA SRX498803

Supplementary file Size Download File type/resource
GSM1356189_TATCGT_minus_cutCount.txt.gz 12.8 Mb (ftp)(http) TXT
GSM1356189_TATCGT_plus_cutCount.txt.gz 12.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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