|
| Status |
Public on Apr 25, 2016 |
| Title |
Dvir MSL1 male replicate B |
| Sample type |
SRA |
| |
|
| Source name |
third instar larva
|
| Organism |
Drosophila virilis |
| Characteristics |
developmental stage: third instar
Sex: male
chip antibody: polyclonal MSL1 antibody raised against the N-terminus (AA1-265)
|
| Growth protocol |
Fly strains were reared at room temperature with standard medium. D. virilis stock number (UCSD): 15010-1051.00
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Inverted 3rd instar larva were fixed, dissolved in RIPA buffer and sonicated 16 x 30 sec using a Branson 250 sonicator at 40 pulse, intensity 5, and chromatin immunoprecipiatet with the respective antibody. (see PMID: 20620954 for details).
Libraries were prepared according to Illumina's instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were aligned to the genome (version dm3 for D. melanogaster samples; version Dvir1.2 for D. virilis samples) using bowtie (v2.0.5) with standard parameters.
Reads with mapping quality < 5 were discarded.10 bp) using the bamCoverage module of the deepTools suite (https://deeptools.github.io; PMID: 247994360
Peak calling was done with MACS2 (v. 2.0.10).
Genome_build: dm3; Dvir1.2
Supplementary_files_format_and_content: Bigwig files were generated using the bamCoverage module of deepTools (https://github.com/fidelram/deepTools), normalizing to 1x coverage with the parameters -f 200 --binSize 10 --normalizeTo1x [158736537 for D.mel | 189205863 for D. vir]
|
| |
|
| Submission date |
Sep 11, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Friederike Dündar |
| E-mail(s) |
frd2007@med.cornell.edu
|
| Organization name |
Weill Cornell Medicine
|
| Department |
Physiology & Biophysics
|
| Lab |
Applied Bioinformatics Core
|
| Street address |
1300 York Ave
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL13313 |
| Series (1) |
| GSE61340 |
ChIP-seq of MSL1 in male and female fly samples |
|
| Relations |
| BioSample |
SAMN03031791 |
| SRA |
SRX699549 |
