 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 12, 2021 |
| Title |
DGRP_28239 |
| Sample type |
SRA |
| |
|
| Source name |
Whole fly brain
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Brain
genotype: DGRP_28239
age: Young adults (1-3 days)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Brains were dissected from one male and one female fly in PBS. Next, 50μl cold lysis buffer was added (10 mM Tris‐HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA‐630). After spinning down at 800g, supernatant was discarded and transposition mix was addded, followed by general omniATAC-seq
omniATAC-seq
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
cleaning with fastqc (1.1.2)
mapping with bowtie2 (2.2.6) on the sample's genome (i.e. mutating the default dm6 according to the VCF of the DGRP line)
peak calling with MACS2 (20160920) - per sample
features counted using Subread (1.4.6) on the merged peaks without repeats
counts normalized based on size-factors with DESeq2
Genome_build: dm6
Supplementary_files_format_and_content: count matrix: read-counts per peak and sample (size-factor normalized)
Supplementary_files_format_and_content: count matrix + genotypes: The first 47 columns are the read counts in peaks, the remaining columns are the genotypes for the overlapping SNPs
|
| |
|
| Submission date |
Aug 04, 2021 |
| Last update date |
Oct 12, 2021 |
| Contact name |
Gert Hulselmans |
| E-mail(s) |
[email protected]
|
| Organization name |
VIB
|
| Department |
Center for Brain and Disease Research
|
| Lab |
Laboratory of Computational Biology
|
| Street address |
Herestraat 49 PO Box 602
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE181494 |
Bulk ATAC-seq on whole brain across DGRP lines (homozigous fly lines) |
|
| Relations |
| BioSample |
SAMN20585401 |
| SRA |
SRX11651254 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
