|
| Status |
Public on Jun 13, 2024 |
| Title |
pupe gypsy2 insert 4C-seq Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
pupal imaginal leg discs
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: pupal imaginal leg discs
genotype: insertion gypsy
|
| Growth protocol |
Drosophila Melanogaste flies gtown at 20°C on, standard medium
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
4C-seq was performed according to Denaud et al (see Material and Methods)
Libraries were preapred according the protocol the illumina kit (illumina 20015964)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
pupegypsyenh1
|
| Data processing |
*library strategy: 4C-seq
4C sequencing were split by viewpoint by mapping the reads to the 4C primer sequences using a custom python script adapted from Grob et al. Genome Biology, 2012
4C primer sequences and genomic sequences until the next restriction site were trimmed from the reads using a custom python script adapted from Grob et al. Genome Biology, 2012
Split libraries were aligned to DM6 genome using bowtie alignment software
The aligned reads were mapped to restriction fragments and genomic bins of 1kb size using HiCdat to obtain tabular files describing the number of reads (i.e. contact frequencies) for a given fragment or genomic bin, respectively
All subsequent analysis steps have been conducted using R.
Assembly: dm6
|
| |
|
| Submission date |
Nov 09, 2023 |
| Last update date |
Jun 13, 2024 |
| Contact name |
Bernd Schuettengruber |
| E-mail(s) |
bernd.schuttengruber@igh.cnrs.fr
|
| Organization name |
Institute de Génétique Humaine
|
| Lab |
Cavalli
|
| Street address |
141, rue de la cardonille
|
| City |
Montpellier |
| ZIP/Postal code |
34396 |
| Country |
France |
| |
|
| Platform ID |
GPL25244 |
| Series (1) |
| GSE247377 |
A PRE loop at the dac locus acts as a topological chromatin structure that restricts and specifies enhancer promoter communication |
|
| Relations |
| BioSample |
SAMN38128670 |
| SRA |
SRX22390901 |
