|
| Status |
Public on Nov 20, 2021 |
| Title |
Dam-PolII expression with twi2xPE-GAL4 promoter replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Drosophila embryonic DNA
|
| Organism |
Drosophila melanogaster |
| Characteristics |
expression: Dam-PolII
promoter: twi2xPE-GAL4
replicate: 1
|
| Growth protocol |
Embryos were collected over a 4 h period and aged at 25°C to stage 10-13, followed by dechorionation in 2% sodium hypochlorite solution for 2 min and subsequent washing steps in PBS. A total of 50 µl embryos per sample was used as starting material.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted (QIAGEN Blood and Tissue DNA extraction kit) and methylated DNA was processed and amplified as previously described (Choksi et al., 2006; Sun et al., 2003), with the following modifications.
Purified PCR products were used for PCR-free library preparation, followed by pair-end sequencing on Illumina HiSeq X Ten platform (BGI Tech Solutions, Hong Kong).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
GATC_counts.txt
Sample td1
|
| Data processing |
Library strategy: DAMID-seq
Basecalls performed using CASAVA version 1.4
Reads were aligned to the dmel r6.21 genome assembly using Bowtie2 (–very-sensitive-local)
Counts of reads mapped on edge to GATC fragments were generated using a script (GATC_mapper.pl) from DamID-Seq pipeline (Maksimov et al.,2016).
GATC sites were merged into peaks following the methods prescribed in a previous study (Tosti et al.,2018). In brief, logFC for individual GATCs were generated using Limma (Jeb versus Dam and DN versus Dam) (P<1e-5) and the GATC sites were merged into peaks based on median GATC fragment distance in the Drosophila genome using mergeWindows and combineTests function from the csaw package (Lun and Smyth, 2016).
Genome_build: dmel r6.21
Supplementary_files_format_and_content: GATC raw counts text files
Supplementary_files_format_and_content: peak text files
|
| |
|
| Submission date |
Nov 15, 2021 |
| Last update date |
Nov 20, 2021 |
| Contact name |
Erik Larsson |
| E-mail(s) |
erik.larsson@gu.se
|
| Organization name |
University of Gothenburg
|
| Street address |
Medicinaregatan 9A
|
| City |
Gothenburg |
| ZIP/Postal code |
40530 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL23702 |
| Series (1) |
| GSE188907 |
DamID transcriptional profiling identifies the Snail/Scratch transcription factor Kahuli as an Alk target in the Drosophila visceral mesoderm |
|
| Relations |
| BioSample |
SAMN23168990 |
| SRA |
SRX13144593 |
