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| Status |
Public on May 21, 2024 |
| Title |
HiC, PS312, J2, rep1 |
| Sample type |
SRA |
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| Source name |
PS312
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| Organism |
Pristionchus pacificus |
| Characteristics |
source: whole worm
Sex: hermaphrodite
strain: PS312
developmental stage: J2
construction protocol: Arima HiC+ kit for high coverage
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| Treatment protocol |
Larvae were treated with 2% formaldehyde for 30 minutes, washed with M9, collected by centrifugation, flash frozen with liquid nitrogen, and stored at -80˚C until extract preparation.
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| Growth protocol |
Pristionchus pacificus J2 larvae were isolated by filtering mixed stage worms through a 20 micron nylon mesh, and collecting the flow through. Oscheius tipulae early stage synchronized larvae were isolated by bleaching gravid adults, hatching embryos in M9, and growing synchronized L1 larvae on NGM plates supplemented agarose at 22˚C for 24 hours.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Larvae were resuspended in PBS with 1 mM PMSF. A mortar and pestle (BioSpec Products, catalog # 206) was placed on dry ice and filled with liquid nitrogen. Drops of larvae were pipetted into the mortar, and pulverized into a fine powder while submerged in liquid nitrogen. Powdered larvae were crosslinked as described in the Arima Hi-C+ High Coverage Kit (A101030), and Hi-C was performed as per the manufacturer’s instructions.
Library preparation was performed with the KAPA Hyper Prep Kit (KK8502) as per Arima’s instructions.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
hic files were generated using Juicer (version 1.5.7).
Assembly: PRJNA12644 (P. pacificus), PRJNA644888 (O. tipulae)
Supplementary files format and content: hic
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| Submission date |
May 21, 2024 |
| Last update date |
May 21, 2024 |
| Contact name |
Avrami Aharonoff |
| E-mail(s) |
avramiaharonoff@gmail.com
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| Organization name |
New York University
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| Department |
Biology
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| Lab |
Sevinç Ercan
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| Street address |
29 Washington Place
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10003 |
| Country |
USA |
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| Platform ID |
GPL34494 |
| Series (1) |
| GSE267963 |
SMC-mediated dosage compensation in C. elegans evolved in the presence of an ancestral nematode mechanism [Hi-C] |
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| Relations |
| BioSample |
SAMN41471101 |
| SRA |
SRX24619858 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8282557_HiC_30_JK88_PS312_J2_rep1.hic |
403.7 Mb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
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