|
| Status |
Public on Jun 17, 2015 |
| Title |
FAIRE_Dvir_EA |
| Sample type |
SRA |
| |
|
| Source name |
eye-antennal imaginal disc
|
| Organism |
Drosophila virilis |
| Characteristics |
developmental time point: third instar wandering larvae
tissue: eye-antennal imaginal disc
genotype: Dvir\wild-type
stock: UCSD: 15010-1051.118
|
| Treatment protocol |
FAIRE-Seq was perfomed in accordance to (Giresi et al. 2007). Eye-antennal imaginal discs were dissected in PBT and cross-linked in 4% formaldehyde for 10 min. Chromatin was isolated using a 3-step lysis protocol and next it was subjected to a ten-cycle sonication (30 seconds on/off).
|
| Growth protocol |
All flies were raised at 25 degrees Celsius on standard fly food
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nucleosome-depleted regions were extracted with phenol/chloroform followed by ethanol precipitation and RNAse A treatment.
Libraries were prepared for sequencing using standard Illumina Truseq protocols
|
| |
|
| Library strategy |
FAIRE-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads with residual adapter sequences were discarded (FastX cliper version 0.012 option -M15)
Reads were mapped against their own-species genome by Bowtie2 (default parameters)
Species alignments were converted to D.melanogaster coordinates by liftOver tool from UCSC (minMatch=0.1)
F-Seq (Boyle et al. 2008) was used to detect nucleosome-free regions in relation to background signal (parameters l=200)
HT-Seq was used to count the number of reads falling within a called peak
Genome_build: Drosophila melanogaster FB5
Supplementary_files_format_and_content: Peak position and original as well as normalized counts
|
| |
|
| Submission date |
Jul 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Stein Aerts |
| Organization name |
KULeuven
|
| Department |
Center for Human Genetics
|
| Lab |
Laboratory of Computational Biology
|
| Street address |
Herestraat 49
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL13313 |
| Series (1) |
| GSE59706 |
Identification of lineage-specific cis-regulatory modules associated with variation in transcription factor binding and chromatin activity using Ornstein-Uhlenbeck models |
|
| Relations |
| BioSample |
SAMN02934559 |
| SRA |
SRX660268 |
