|
| Status |
Public on Nov 30, 2015 |
| Title |
PARP-1 ChIP-seq replicate 4 |
| 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 |
SAMN02697226 |
| SRA |
SRX498804 |
