|
| Status |
Public on Jul 25, 2023 |
| Title |
Male_WT_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Anopheles gambiae |
| Characteristics |
developmental stage: Pupa
Sex: Male
genotype: WT
tissue: whole organism
|
| Growth protocol |
A. gambiae mosquitoes were maintained in standard insectary conditions (26–28°C, 75–80% humidity, and 12-/12-h light/dark cycle).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The experiment was performed with flash frozen tissues, which were homogenized in cold PBS and passed through a cell strainer. The cell suspension was counted and 50,000 cells were used for each reaction. The libraries were generated according to the following protocol: 10.1002/0471142727.mb2129s109. We used Tn5 prepared by the IMB protein production core facilty.
ATAC-seq libraries were amplified using NEBNext Ultra II Q5 Master Mix with standard protocols and 15 PCR cycles. Libraries were cleaned up using 1.3 volume Ampure XP beads and pooled together for paired-end sequencing.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Male_WT_Rep3
|
| Data processing |
Reads were trimmed with cutadapt (v4.0) to remove Illumina adapter sequences.
Trimmed reads were mapped to the ensembl AgamP4 genome with bowtie2 (v2.4.5)
Multimapping and duplicate reads were discarded using BamUtil (v1.0.14) and Samtools (v1.10)
Coverage signal tracks (bigWigs) of alignments were generated using Samtools (v1.10) and DeepTools (v3.5.1)
Peaks were called with MACS2 version (v2.1.2).
DiffBind (v3.4.0) was used to determine differential binding, with normalization by full library size. Only peaks with FDR<0.05 were considered as differentially bound.
Assembly: AgamP4
Supplementary files format and content: bigWig files, containing CPM normalized coverage signals of primary alignments
|
| |
|
| Submission date |
Aug 05, 2022 |
| Last update date |
Jul 25, 2023 |
| Contact name |
Frank Rühle |
| E-mail(s) |
f.ruehle@imb-mainz.de
|
| Organization name |
Institute of Molecular Biology (IMB)
|
| Department |
Bioinformatics Core Facility
|
| Street address |
Ackermannweg 4
|
| City |
Mainz |
| ZIP/Postal code |
55128 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22033 |
| Series (2) |
| GSE210626 |
SOA confers X chromosome dosage compensation in Anopheles gambiae mosquitoes (ATAC-Seq) |
| GSE210630 |
SOA confers X chromosome dosage compensation in Anopheles gambiae mosquitoes |
|
| Relations |
| BioSample |
SAMN30167105 |
| SRA |
SRX16881259 |
