|
| Status |
Public on Oct 11, 2018 |
| Title |
RNApol-II_Ctrl |
| Sample type |
SRA |
| |
|
| Source name |
Undamaged Wing Disc
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Wing Disc
developmental stage: Third instar larvae
condition: Undamaged
chip antibody: RNA polII
|
| Growth protocol |
Flies were grown on standard media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We isolated 100 wing discs per sample (early control and regeneration). Discs were fixed, pooled in 700 μl of sonication buffer (10 mM Tris-HCl, pH 8.0, 2 mM EDTA and 1 mM EGTA) and processed as described (Pérez-Lluch et al. 2011). Immunoprecipitations were performed in RIPA buffer and using 1 μg of the corresponding antibody. Immunocomplexes were recovered by incubation with Invitrogen Protein A magnetic beads for 2 h. The beads were washed three times in RIPA, once in lithium chloride buffer and twice in TE buffer. After, an RNase treatment was done and samples were decrosslinked at 65⁰C overnight by adding Proteinase K. Samples were purified with Qiagen MinElute Kit and eluted in Gibco water.
HiSeq2000
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
transcriptomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
PolyA RNA
|
| Data processing |
Data was processed using chip-nf pipeline (available at https://github.com/guigolab/chip-nf).
Reads were continuously mapped to the fly genome (dm6) using GEM mapper.
Duplicated reads were removed using Picard (http://broadinstitute.github.io/picard/).
Fragment length was estimated using SPP.
Peak calling was performed using MACS2.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: bigWig, narrowPeak (bed)
|
| |
|
| Submission date |
Jun 11, 2018 |
| Last update date |
Oct 11, 2018 |
| Contact name |
Montserrat Corominas |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Barcelona
|
| Department |
Genètica, Microbiologia i estadística
|
| Street address |
Diagonal 643
|
| City |
Barcelona |
| State/province |
Catalonia |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE102841 |
Time-course chromatin accessibility and transcriptome in regeneration |
| GSE115630 |
ChIP-seq for active enhancers marks at early regeneration |
|
| Relations |
| BioSample |
SAMN09395157 |
| SRA |
SRX4194144 |
