|
| Status |
Public on Nov 09, 2022 |
| Title |
wt_13-17hr_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
13-17hr old embryos
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: 13-17hr old embryos
genotype: wt
normalization factor: 0.0372213821356274
|
| Growth protocol |
Drosophila embryos were grown on standard medium at 25˚C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were purified from embryos of the desired genotype and 25000 nuclei were used for the tagmentation reaction.
Libraries were prepared according to Active Motif's instructions accompanying the ATAC-seq kit (#53150).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads from fastq files were aligned to the dm6 genome (and to the D. pseudoobscura dp3 genome for subsequent normalization) using STAR (Dobin et al., 2013). Only sequences that mapped uniquely to the genome with a maximum of two mismatches were considered for further analyses.
Bam files were used as inputs to run Bioconductor packages.
The STAN Bioconductor package (Zacher et al., 2014) was used to define the location of regions associated with low, intermediate and high DNA accessibility in wild-type embryos.
Datasets were normalized based on total read number per million reads.
Assembly: dm6
Supplementary files format and content: Normalized bigwig files (bin size = 1) were generated with deepTools (Ramirez et al., 2016).
|
| |
|
| Submission date |
Aug 01, 2022 |
| Last update date |
Nov 09, 2022 |
| Contact name |
Jürg Müller |
| Organization name |
Max Planck Institute of Biochemistry
|
| Street address |
Am Klopferspitz
|
| City |
Martinsried |
| State/province |
Bavaria |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE210232 |
PR-DUB preserves Polycomb repression by preventing excessive accumulation of H2Aub1, an antagonist of nucleosome stacking (ATAC-Seq) |
| GSE210236 |
PR-DUB preserves Polycomb repression by preventing excessive accumulation of H2Aub1, an antagonist of nucleosome stacking |
|
| Relations |
| BioSample |
SAMN30081271 |
| SRA |
SRX16751649 |
