|
| Status |
Public on Jun 13, 2024 |
| Title |
Larv gypsy3 insertion HiC Repli1 |
| Sample type |
SRA |
| |
|
| Source name |
larval imaginal leg discs
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: larval imaginal leg discs
genotype: insertion gypsy
|
| Growth protocol |
Drosophila Melanogaste flies gtown at 20°C on, standard medium
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
HiC was performed according the protocol of the EpiTect Hi-C Kit from Quiagen
Libraries were preapred according the protocol of the EpiTect Hi-C Kit from Quiagen
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
gypsy3_1
|
| Data processing |
Hi-C data was processed using the schic2 pipeline (https://github.com/tanaylab/schic2). In brief, raw sequencing reads were mapped independently to the reference genome using Bowtie2 in local alignment mode. The uniquely mapped (MAPQ > 36) reads were translated into a pair of fragment-ends (fends) by associating each read with its downstream fend. PCR duplicates and reads mapping to the same restriction fragment were excluded.
Assembly: dm6
Supplementary files format and content: Each processed file represent pairwise information of the observed genome contacts in the form of a "misha" (https://github.com/tanaylab/misha) database entry and can be further analyzed using the "shaman" pipeline (https://github.com/tanaylab/shaman).
|
| |
|
| Submission date |
Nov 09, 2023 |
| Last update date |
Jun 13, 2024 |
| Contact name |
Bernd Schuettengruber |
| E-mail(s) |
[email protected]
|
| 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 |
GPL32218 |
| 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 |
SAMN38128672 |
| SRA |
SRX22390893 |
