|
| Status |
Public on Jan 17, 2013 |
| Title |
OSC DHS-seq Input |
| Sample type |
SRA |
| |
|
| Source name |
OSC cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: OSC cells
sample type: PCR amplified DNaseI digested genomic DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
5-7 10^7 cells were harvested. DNase treatment was done as in (L. Cappabianca, H. Thomassin, R. Pictet, T. Grange, Genomic footprinting using nucleases., Methods in molecular biology (Clifton, N.J.) 119, 427-42 (1999)). For size selection (~120bp) a sucrose gradient was emplyed (SW TI40, 30000rpm, 16h). Library was constructed following instructions of NEBNext® DNA Library Prep Reagent Set for Illumina® (NEB; cat. no. E6000L). Library amplifcation was done using KAPA Library Amp Real Time (KAPA biosystems: cat.no. KK2701).
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
PCR amplified DNaseI digested genomic DNA
|
| Data processing |
Basecall where performed using Real-Time Analysis (RTA) version > 1.12.4.2 or CASAVA 1.9.1
Reads were mapped to the dm3 genome using bowtie (bowtie -f -v 3 -m 1 --best --strata --quiet -S INDEX -) excluding chrU, chrUextra, and chrM. We estimated the enrichment and p-values for specific genomic regions using the cDNA and the input together with a hypergeometric test. To call peaks we also used MACS14 with default parameters and an FDR cutoff of 5%.
Genome_build: dm3
|
| |
|
| Submission date |
Sep 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Gerlach |
| E-mail(s) |
[email protected]
|
| Organization name |
Boehringer Ingelheim RCV GmbH & Co KG
|
| Department |
Global Computational Biology and Digital Sciences
|
| Street address |
Dr.-Boehringer-Gasse 5-11
|
| City |
Vienna |
| ZIP/Postal code |
1121 |
| Country |
Austria |
| |
|
| Platform ID |
GPL11203 |
| Series (1) |
| GSE40739 |
Genome-wide quantitative enhancer activity maps identified by STARR-seq |
|
| Relations |
| SRA |
SRX187084 |
| BioSample |
SAMN01176869 |
