|
| Status |
Public on Sep 17, 2023 |
| Title |
D429F01_Hi-C p50_PD-D1-2h |
| Sample type |
SRA |
| |
|
| Source name |
full embryo
|
| Organism |
Bombyx mori |
| Characteristics |
tissue: full embryo
strain: p50
time: 1-2h
|
| Growth protocol |
20-30 p50 diapaused eggs harvest after release at 25°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Eggs were glued in a Petri dish filled with 3% formaldehyde before chorions were poked with a fine needle to allow embryos fixation for 30 min. After quenching, embryos were dissected out of chorion with fine forceps before frozen at -80°C and processed with Arima-HiC+ kit from Arima genomics.
Sequencing libraries were prepared using the KAPA HyperPrep Library Preparation Kit complemented with Illumina TruSeq DNA UD Indexes. Libraries were amplified using 8-14 cycles on the thermocycler. Post amplification libraries were size selected at 250-600bp in length using SPRIselect beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity screenTapes.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Hi-C
|
| Data processing |
Library were sequenced on Novaseq.
Adapter sequences were trimmedfrom reads using trimgalore.
Hi-C reads were processed and filtered using the HiCPro suite.
Matrices files have been generated using the cooler suite and format.
Assembly: Bmori_v3 or Bmori_4
Supplementary files format and content: multi-resolution cooler
|
| |
|
| Submission date |
Mar 28, 2023 |
| Last update date |
Sep 17, 2023 |
| Contact name |
Héloïse Muller |
| E-mail(s) |
heloise.muller@curie.fr
|
| Organization name |
Institut Curie
|
| Lab |
UMR3664
|
| Street address |
26 rue d'Ulm
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL29210 |
| Series (2) |
| GSE228400 |
Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori [Hi-C embryo] |
| GSE228401 |
Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori |
|
| Relations |
| BioSample |
SAMN33954928 |
| SRA |
SRX19798800 |
