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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 29, 2024 |
| Title |
PromoterHIC_Sham_WT2 |
| Sample type |
SRA |
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| Source name |
DRG
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| Organism |
Mus musculus |
| Characteristics |
tissue: DRG
cell type: DRG neuronal nuclei
genotype: INTACT-AdvillinCre (WT)
treatment: tamoxifen
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| Treatment protocol |
Neuronal nuclei were isolated from mouse sciatic dorsal root ganglia 3 days after sciatic nerve crush (SNC) or sham or in naïve conditions from WT (INTACT-AdvillinCre) and Rad21 KO (INTACT-Scc1flox/flox-AdvillinCre) mice, 14 days after tamoxifen injection.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Neuronal nuclei, expressing nuclear membrane GFP, were immunoisolated via beads bound to anti-GFP.
Nuclei were crosslinked with 2% formaldehyde for 10 min at room temperature. Nuclei were processed for Hi-C using ARIMA Hi-C Genomics kits (A510008). Briefly, chromatin was digested with multiple enzymes, and purified proximity-ligated DNA was sheared using Bioruptor to obtain an average size of 400 bp. After DNA size selection of 200-600 bp, biotin enrichment, end-repair and adapter ligation, Hi-C libraries were prepared starting from 30-65 ng of DNA and 10 PCR cycles, using Swift Biosciences Accel-NGS 2S Plus DNA library kit (21024) and KAPA Library amplification kit (KK2620) or Arima Library preparation module (A303010). In the case of capture Hi-C, precapture Hi-C libraries were prepared starting from 30 ng of DNA and 14 PCR cycles, using KAPA Library amplification kit (KK2620) or Arima Library preparation module (A303010). After preclearing, hybridization and capture were performed using Arima Mouse Promoter Panel (A302020) starting from 1microg of precapture libraries. Promoter Hi-C libraries were amplified with 13 cycles
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
PromoterHIC_Sham_WT2
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| Data processing |
For Hi-C data processing, we used Juicer to generate two hic files (MAPQ > 0 and MAPQ >= 30).
For promoter capture Hi-C data processing, we followed Arima Capture Hi-C V1.4 pipeline (https://github.com/ArimaGenomics/CHiC).
Assembly: mm10
Supplementary files format and content: .hic
Supplementary files format and content: .Rds serialized R objects
Library strategy: promoter capture Hi-C
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| Submission date |
Dec 08, 2023 |
| Last update date |
Aug 29, 2024 |
| Contact name |
Ilaria Palmisano |
| E-mail(s) |
ilaria.palmisano@osumc.edu
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| Organization name |
Ohio State University
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| Street address |
460 West 12th Avenue
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| City |
Columbus |
| State/province |
Ohio |
| ZIP/Postal code |
43210 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE249687 |
Three-dimensional chromatin architecture in DRG neurons following sciatic nerve injury in WT and Rad21 KO mice. |
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| Relations |
| BioSample |
SAMN38331181 |
| SRA |
SRX22585532 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7957379_PromoterHIC_Sham_WT2.Rds.gz |
350.8 Mb |
(ftp)(http) |
RDS |
SRA Run Selector |
| Raw data are available in SRA |
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