|
| Status |
Public on Oct 01, 2015 |
| Title |
PARP-1 ChIP-seq MDA-MB231 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB231
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Breast cancer
passages: 10--15
cell line: MDA-MB231
antibody: Active motif-39559
|
| Growth protocol |
MCF7 and MDA-MB231 cells were obtained from ATCC
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
GSM1517305
Libraries were prepared according to Applied Biosystems protocol for SOLiD 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 5500 Genetic Analyzer |
| |
|
| Data processing |
PARP-1 SOLiD output files were converted to fastq using custom script. Mapped PARP-1 reads to the Human genome (Hg19) using BWA v0.6.1. Estimated the mean PARP1 fragment length of each replicate by computing the offset that gave the highest covariation of read depth between the forward and reverse strands. Estimated PARP1 nucleosome midpoint locations as the read start plus the offset (or minus the offset for those that mapped to the reverse strand. Genome_build: hg19. Supplementary_files_format_and_content: wig files containing counts of mapped fragment midpoints at each genomic position
|
| |
|
| Submission date |
Sep 30, 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 |
GPL16558 |
| Series (1) |
| GSE61916 |
Genome-wide maps of PARP-1-bound nucleosomes (human) |
|
| Relations |
| BioSample |
SAMN03085583 |
| SRA |
SRX718116 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1517306_LN5_chr1.wig.gz |
1.5 Gb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr10.wig.gz |
913.1 Mb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr11.wig.gz |
815.6 Mb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr12.wig.gz |
853.1 Mb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr13.wig.gz |
562.0 Mb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr14.wig.gz |
625.5 Mb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr15.wig.gz |
524.1 Mb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr16.wig.gz |
464.7 Mb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr17.wig.gz |
530.2 Mb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr18.wig.gz |
422.6 Mb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr19.wig.gz |
349.0 Mb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr2.wig.gz |
1.5 Gb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr20.wig.gz |
452.5 Mb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr21.wig.gz |
198.0 Mb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr22.wig.gz |
220.5 Mb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr3.wig.gz |
1.2 Gb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr4.wig.gz |
1.1 Gb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr5.wig.gz |
1.1 Gb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr6.wig.gz |
1.1 Gb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr7.wig.gz |
947.6 Mb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr8.wig.gz |
921.3 Mb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chr9.wig.gz |
639.9 Mb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chrX.wig.gz |
601.0 Mb |
(ftp)(http) |
WIG |
| GSM1517306_LN5_chrY.wig.gz |
9.0 Mb |
(ftp)(http) |
WIG |
| GSM1517306_YFM_Nov19_12_CS_Ln5_results.txt.gz |
3.3 Gb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
