|
| Status |
Public on Dec 22, 2017 |
| Title |
No-IgG Triple-crosslinked |
| Sample type |
SRA |
| |
|
| Source name |
S2R+
|
| Organism |
Drosophila melanogaster |
| Characteristics |
antibody: No-IgG
|
| Treatment protocol |
Cells were crosslinked with dimethyl adipimidate and ethylene glycol bis(succinimidyl succinate) for at room temperature for 10 minutes prior to the addition of 1% formaldehyde followed by an additional 10 minute incubation at room temperature.
|
| Growth protocol |
M3+BPYE media at 25°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with rabbit IgG antibody.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Protein-DNA complex
ChIP-exo
|
| Data processing |
Basecalls performed using Bcl2FastQ version 2.16.0
Sequenced reads were masked for low-quality sequence, then mapped to dm3 whole genome using bwa mem 0.7.9a,0.7.12 with the default parameters.
Replicates were megred and and only the 5' end of read1 was kept.
Tag directories were created in homer with a fragment length of 1.
BedGraph files were generated using the Homer makeUCSCfile command with reads normalized to 1E7
Genome_build: dm3
Supplementary_files_format_and_content: bedGraph files for each sample were generated using homer's makeUCSCfile function by normalizing to 1E7 and keeping strand information.
|
| |
|
| Submission date |
Oct 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
David S Gilmour |
| E-mail(s) |
dsg11@psu.edu
|
| Organization name |
Penn State University
|
| Street address |
465 North Frear
|
| City |
University Park |
| State/province |
Pennsylvania |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE105009 |
GFZF, a glutathione S-transferase protein implicated in cell cycle regulation and hybrid inviability, is a transcriptional co-activator |
|
| Relations |
| BioSample |
SAMN07788350 |
| SRA |
SRX3287356 |
