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| Status |
Public on Sep 25, 2024 |
| Title |
HN_fHiC_006_Nostim_1h_5HSIII_ILC2_rep2 |
| Sample type |
SRA |
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| Source name |
lung
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| Organism |
Mus musculus |
| Characteristics |
tissue: lung
cell type: ILC2
genotype: 5HSIII-KO
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
A detailed protocol to generate HiC libraries can be obtained at PMID:25497547 and PMID:26499245. For focused HiC-seq, we designed 1490 probes targeting chr11:53,250,000 – 54,250,000 (length: 1Mb) containing type 2 cytokine locus.
A detailed protocol to generate HiC libraries can be obtained at PMID:25497547 and PMID:26499245. For focused HiC-seq, we designed 1490 probes targeting chr11:53,250,000 – 54,250,000 (length: 1Mb) containing type 2 cytokine locus.
focused HiC
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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 |
The initial Hi-C data processing was done with HOMER 4.11.1. The MboI restriction sites used for self ligation (GATC) were trimmed from the FastQ files using “homerTools trim” function. The trimmed reads were mapped onto mm10 using Bowtie 2.4.5. The paired-end tag directories were created using “makeTagDirectory” command, which also generated several quality control analysis files. The .hic files were created using HOMER function “tagDir2hicFile.pl” with Juicer 1.6 and visualized with Juicebox 1.9.8.
Assembly: mm10
Supplementary files format and content: .hic files
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| Submission date |
May 01, 2024 |
| Last update date |
Dec 05, 2024 |
| Contact name |
Hiroyuki Nagashima |
| E-mail(s) |
hiroyuki.nagashima@nih.gov
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| Phone |
3013383729
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| Organization name |
NIH
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| Street address |
10 Center Dr, Room 13C120
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| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE266345 |
Remodeling of Il4-Il13-Il5 locus underlies selective gene expression (fHiC) |
| GSE266349 |
Remodeling of Il4-Il13-Il5 locus underlies selective gene expression |
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| Relations |
| BioSample |
SAMN41151429 |
| SRA |
SRX24423316 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8245390_HN_fHiC_006_Nostim_1h_5HSIII_ILC2_rep2.hic |
461.4 Mb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
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