|
| Status |
Public on Oct 14, 2019 |
| Title |
Input_Dvir_female |
| Sample type |
SRA |
| |
|
| Source name |
Female 3rd instar larvae
|
| Organism |
Drosophila virilis |
| Characteristics |
strain: San Diego stock center, stock number: 15010-1051.0
chip antibody: none (input)
tissue: anterior portion of third instar larvae
Sex: female
|
| Growth protocol |
D. melanogaster and D. virilis flies were maintained in standard Drosophila medium. D. busckii flies were additionally fed with instant Drosophila medium (Formula 4-24, Carolina Biological Supply Company, catalog number 173202) mixed with instant potato powder on top of the standard Drosophila medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq: Larvae were dissected and the front part fixed at RT for 15 min with 0.2% formaldehyde. Chromatin was extracted using a sucrose cushion followed by Micrococcal Nuclease treatment and 10 cycles of sonication in a Bioruptor Pico. The lysate was clarified by centrifugation before immunoprecipitation, washes, elution by reverse crosslinking at 65deg for 16h. After RNaseA and proteinaseK treatment, the DNA from input and immunoprecipitation was purified using phenol-chloroform extraction and ethanol precipitation.
NEB Next Ultra II
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
ChIP-seq: Data processing included sequencing quality and adaptor trimming of paired-end reads using trim_galore v0.4, mapping individual replicates using bwa v0.7.12 followed by sorting and indexing of bam files using samtools-1.2. The coverage of mapped reads was calculated using deeptools v2.0.1 with settings `-bs 10 --normalizeTo1x {EFFECTIVE_GENOME_SIZE}`. We defined the effective genome size as the total genome size minus the number of Ns which is 117 Mb and 188 Mb for D. busckii and D. virilis, respectively. Log2fold ratios of merged replicates over the input sample was calculated using bamCompare with settings `-bs 10 --scaleFactorsMethod SES`.
Genome_build: Dvir_HiC, Dbus_HiC, Dm6
Supplementary_files_format_and_content: ChIP-seq: bigWig files of mapped reads of individual replicates (SampleName.bw) and bigWig files of log2fold ratios of merged replicates over the input sample (SampleName-Input.bw).
|
| |
|
| Submission date |
Oct 02, 2018 |
| Last update date |
Oct 14, 2019 |
| Contact name |
Asifa Akhtar |
| E-mail(s) |
akhtarlab_data@ie-freiburg.mpg.de
|
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
|
| Department |
Chromatin Regulation
|
| Lab |
Akhtar Lab
|
| Street address |
Stuebeweg 51
|
| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL25633 |
| Series (2) |
| GSE120750 |
Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling [ChIP-seq] |
| GSE120752 |
Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling |
|
| Relations |
| BioSample |
SAMN10166443 |
| SRA |
SRX4786518 |
