|
| Status |
Public on Nov 03, 2020 |
| Title |
Dpn_ChIP_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
3rd instar larval CNS
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: larval brains with neural stem cell hyperplasia
chip antibody: Homemade Deapan antibody
genotype: grhGal4;UAS-dpn, UAS-m<gamma>
|
| Treatment protocol |
CNSs from 3rd instar wandering larvae were dissected in ice cold PBS
|
| Growth protocol |
Expanded population of NSC like cells were obtained by overexpressing UAS-dpn,UAS-mγ using neural stem cell specific grhGal4 and maintained at 25°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin lysate was crosslinked with 1%FA and quenched with Glycine, chromatin was fragmented using bioruptor and immunoprecipitated chromatin was purified using Qiagen PCR purification kit.
Libraries were prepared according to Ion Torrent instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
Genome-wide Deadpan binding replicate 2
BED file with intersection of replicate 1 and replicate 2
|
| Data processing |
Fastq reads were mapped to UCSC/dm3 genome (archive-2015-07-17-14-30-40) downloaded from iGenomes using bowtie2 version 2.2.8
Bedgraphs of mapped reads were generated by bedtools genomecov (v2.25.0)
Reads that overlapped with dm3 repeat elements (downloaded from UCSC,) were removed from bam files prior to peak calling using bamtools intersect
Peak calling was performed with macs2 over input (-p 0.05, version 2.1.0.20140616)
Genome wide peak distribution was performed with the pavis tool
Genome_build: dm3
Supplementary_files_format_and_content: Bed file containing overlapping peaks from replicates over input
|
| |
|
| Submission date |
Dec 10, 2019 |
| Last update date |
Nov 04, 2020 |
| Contact name |
Christos Delidakis |
| E-mail(s) |
delidaki@imbb.forth.gr
|
| Phone |
+302810 391112
|
| Organization name |
Foundation for Research and Technology - Hellas
|
| Department |
Institute of Molecular Biology and Biotechnology (IMBB)
|
| Lab |
Neural development
|
| Street address |
Nikolaou Plastira 100
|
| City |
Heraklion |
| State/province |
Crete |
| ZIP/Postal code |
GR-70013 |
| Country |
Greece |
| |
|
| Platform ID |
GPL19528 |
| Series (2) |
| GSE141792 |
Genome-wide occupancy of Hes protein Deadpan in neural stem cells from Drosophila 3rd instar larvae |
| GSE141794 |
Hes protein Deadpan in neural stem cells from Drosophila 3rd instar larvae |
|
| Relations |
| BioSample |
SAMN13528026 |
| SRA |
SRX7341042 |
