|
| Status |
Public on Aug 27, 2020 |
| Title |
w1118 ChIP-seq rep1 |
| Sample type |
SRA |
| |
|
| Source name |
fly heads
|
| Organism |
Drosophila melanogaster |
| Characteristics |
age: day 14
genotype: w;;
antibody: anti-V5 (Sigma A7345)
|
| Growth protocol |
Flies were maintained on standard cornmeal-agar food at 25 °C in a 12 h:12 h light-dark cycle and under controlled humidity.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
~8000 14-day-old flies per sample were collected 2 h before lights-on (ZT22), frozen in liquid nitrogen and maintained at -80 °C until processed. Heads were collected using metal sieves, and then, 1 ml of heads was ground in liquid nitrogen and homogenized 30 times in NE Buffer with 1% PFA. Lysates were clarified from sonicated nuclei and Fer2-DNA complexes were isolated with antibody.
Libraries were prepared with 0,5 to 0,7 ng of ChIP-enriched DNA as starting material and processed using the Illumina TruSeq ChIP kit according to the manufacturer’s specifications, at the iGE3 Genomics Platform in Geneva. The libraries were validated on a Tapestation 2200 (Agilent) and a Qubit fluorometer (Invitrogen - Thermo Fisher Scientific). Single reads of 50 bp were generated using the TruSeq SBS HS v3 chemistry on an Illumina HiSeq 2500 sequencer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
ChIP-seq reads were aligned to the dm3 genome assembly using Bowtie2 with default settings
Peaks were called using MACS2 with default settings (q-value=0.05) by comparing each Fer2::GFP::V5 ChIP sample (N=2) to each w1118 ChIP sample (N=2; negative control). The 267 shared peaks overlapping in all the four FER2 ChIP vs w1118 ChIP comparisons were selected as confident peaks.
Genome_build: dm3
Supplementary_files_format_and_content: peak text files generated by MACS2
|
| |
|
| Submission date |
Aug 26, 2020 |
| Last update date |
Aug 27, 2020 |
| Contact name |
Federico Miozzo |
| Organization name |
University of Geneva
|
| Street address |
30 Quai Ernest-Ansermet, CH-1211
|
| City |
Geneva |
| ZIP/Postal code |
1205 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17275 |
| Series (2) |
| GSE156892 |
Genome-wide map of the binding sites of the transcription factor Fer2 in the fly brain |
| GSE156893 |
Fer2 in the fly brain |
|
| Relations |
| BioSample |
SAMN15912780 |
| SRA |
SRX9008800 |
