|
| Status |
Public on Jul 01, 2023 |
| Title |
HiC_S2_luc_KD_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
S2 (Schneider 2)
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2 (Schneider 2)
cell type: Late embryonic derived S2 cells
treatment: WT
|
| Treatment protocol |
S2 cells were treated for RNAi-mediated depletion, T7-driven synthesis (Fermentas TranscriptAid™ T7 High Yield Transcription Kit) of double-stranded RNAs (dsRNA) specific for Mes4/NSD, Hypb/dSET2 or luc were used. 400 µg of dsRNA were added to 36 millions cells in 10 mL media without FBS following for 2h at 25°C before adding FBS. Depletion was optimized for incubation of 4 days and cells were then harvested.
|
| Growth protocol |
Schneider 2 (S2) Drosophila cells were cultured in Schneider Drosophila medium complemented with 10% heat-inactivated FBS and 1% pen-strep
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ARIMA HiC Kit
KAPA hyperprep
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
DNBSEQ-T7 |
| |
|
| Data processing |
alignment: Juicer version 1.6; BWA 0.7.17-r1188; openjdk version 1.8.0_302
Assembly: genome_version : dm6-r6.32
Supplementary files format and content: HiC contact matrix (.hic format)
|
| |
|
| Submission date |
Jul 28, 2022 |
| Last update date |
Jul 01, 2023 |
| Contact name |
Olivier Cuvier |
| E-mail(s) |
olivier.cuvier@gmail.com
|
| Organization name |
CNRS
|
| Department |
LBME
|
| Lab |
Chromatin Dynamics & Cell proliferation
|
| Street address |
118 route de Narbonne
|
| City |
Toulouse |
| ZIP/Postal code |
31062 |
| Country |
France |
| |
|
| Platform ID |
GPL32518 |
| Series (2) |
| GSE146994 |
Chromatin organization in 3D distinguishes the influences of dMes-4/NSD and Hypb/dSet2 in protecting genes from H3K27me3 silencing |
| GSE209956 |
Chromatin organization in 3D distinguishes the influences of dMes-4/NSD and Hypb/dSet2 in protecting genes from H3K27me3 silencing [Hi-C] |
|
| Relations |
| BioSample |
SAMN30020760 |
| SRA |
SRX16711888 |
