|
| Status |
Public on Jun 14, 2022 |
| Title |
N2_L3_rep2_2 [JK90] |
| Sample type |
SRA |
| |
|
| Source name |
whole worms
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
tissue: whole worms
developmental stage: L3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C: Crosslinked worms were resuspended in 20 ul of PBS per 50ul of worm pellet then dripped into liquid nitrogen containing mortar. The worms were grounded with pestle until fine powder. Grounded worms were crosslinked again in 2% formaldehyde using the TC buffer as described by the Arima Hi-C kit, which uses two 4-base cutters, DpnII and HinfI. The Arima manufacturer’s protocol was followed.
Hi-C: Â Library preparation was performed using the KAPA Hyper Prep Kit using the protocol provided by Arima.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Hi-C: data was mapped to ce10 (WS220) reference genome or its variant that corrosponds to the perturbation using default parameters of the Juicer pipeline version 1.5.7 (Durand et al., 2016).
processed data files format and content: Hi-C: hic matrix files
Assembly: WS220 or its variants based on rex insertion or chromosome fusion
|
| |
|
| Submission date |
Jun 14, 2022 |
| Last update date |
Jun 24, 2022 |
| Contact name |
Jun Kim |
| E-mail(s) |
kimj50@nyu.edu
|
| Phone |
7183094777
|
| Organization name |
NYU
|
| Department |
Biology
|
| Lab |
Ercan
|
| Street address |
100 Washington Square East 1009 Silver Center
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10003 |
| Country |
USA |
| |
|
| Platform ID |
GPL26672 |
| Series (2) |
| GSE168803 |
Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans |
| GSE206065 |
Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans (ChIP-seq and Hi-C data) |
|
| Relations |
| BioSample |
SAMN29039060 |
| SRA |
SRX15887150 |
