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Status |
Public on Nov 21, 2019 |
Title |
brat RNAi neuroblasts replicate 2 (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).
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|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
brat-SBa68-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)
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|
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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 |
SAMN12314264 |
SRA |
SRX6468481 |