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Sample GSM3954657 Query DataSets for GSM3954657
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).
 
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)
 
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

Supplementary file Size Download File type/resource
GSM3954657_brat-H3K4me3-R3-SBa68.count.txt.gz 357.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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