|
| Status |
Public on Nov 21, 2014 |
| Title |
ELAV 6-8h rep1 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryos
|
| Organism |
Drosophila melanogaster |
| Characteristics |
hours after fertilization: 6-8
chip antibody: ELAV
chip antibody vendor: Developmental Studies Hybridoma Bank (DSHB)
chip catalog number: mouse anti-ELAV-9F8A9
chip catalog number: rat anti-ELAV-7E8A10
|
| Growth protocol |
Drosophila melanogaster yw flies were reared in standard cornmeal food at 25C, embryos were collected on apple juice plates.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole embryo nuclei extracts were sonicated and ChIP assays were done using a mix of two anti-ELAV antibodies raised against the entire ELAV protein: mouse anti-ELAV-9F8A9 (DSHB) and rat anti-ELAV-7E8A10 (DSHB).
ChIP-seq libraries were constructed with the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina using NEBNext Multiplex Oligos.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Standard FASTQ files were outputed by CASAVA_v1.8.0
All sequencing reads were aligned to the Drosophila melanogaster reference genome (UCSC dm3 release) using Bowtie version 0.12.7 with parameters -k 1 -m 1 -n 2 --best --strata.
We used the model-based analysis of ChIP-Seq (MACS) peak-finding algorithm version 1.4.1 with default parameters to identify the regions of ELAV ChIP-Seq enrichment over input DNA.
Genome_build: dm3
Supplementary_files_format_and_content: bedGraph files were generated using HOMER software; Scores represent reads per 10 million total reads.
|
| |
|
| Submission date |
Nov 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
UC Berkeley
|
| Street address |
University of California at Berkeley
|
| City |
Berkeley |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE63323 |
ELAV ChIP-seq in Drosophila melanogaster embryos |
|
| Relations |
| BioSample |
SAMN03196574 |
| SRA |
SRX760380 |
