|
| Status |
Public on Nov 21, 2019 |
| Title |
brat RNAi numb RNAi neuroblasts replicate 1 (H3K4me3) |
| Sample type |
SRA |
| |
|
| Source name |
neural stem cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: tumor neuroblasts
tissue: L3 larval brain
chip antibody: H3K4me3 (Millipore 07-473)
|
| Growth protocol |
Larvae were reared on standard fly food until L3 stage (wandering).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
NBs and neurons were isolated according to Harzer et. Al (2013, Nature protocols). Samples were MNase treated.
Libraries were prepared according to Bowman et. Al (2013 BMC Genomics).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
brat-numb-SBa67-H3K4me3.subtractInput.bw
|
| Data processing |
Reads are aligned to dm3 with bowtie2 (v2.2.4).
Coverage tracks are produced with deeptools (v2.5.0.1) by subtracting the respective input (--ratio subtract --normalizeTo1x 121400000 -bs 1).
Reads of ChIP alignments are counted with multiBamCov of bedtools (v2.25.0). H3K4me3 reads are counted in a 500bp region downstream of the first TSS. H3K27me3 reads are counted over the genebody. Flybase 5.44 is used as annotation.
Genome_build: dm3
Supplementary_files_format_and_content: bigwig (coverage subtracted by input); txt (read counts in region)
|
| |
|
| Submission date |
Jul 18, 2019 |
| Last update date |
Nov 21, 2019 |
| Contact name |
Merve Deniz Abdusselamoglu |
| E-mail(s) |
merve.abdusselamoglu@imba.oeaw.ac.at
|
| Organization name |
Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)
|
| Street address |
Doktor. Bohr-Gasse 3
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE134509 |
Genome wide maps of chromatin states of larval Drosophila neural stem cells (NSCs), their progeny and their tumorigenic counterparts |
|
| Relations |
| BioSample |
SAMN12314263 |
| SRA |
SRX6468482 |
