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Sample GSM8245392 Query DataSets for GSM8245392
Status Public on Sep 25, 2024
Title HN_fHiC_008_33_NMU_1h_WT_ILC2_rep2
Sample type SRA
 
Source name lung
Organism Mus musculus
Characteristics tissue: lung
cell type: ILC2
genotype: WT
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
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
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
 
Submission date May 01, 2024
Last update date Dec 05, 2024
Contact name Hiroyuki Nagashima
E-mail(s) hiroyuki.nagashima@nih.gov
Phone 3013383729
Organization name NIH
Street address 10 Center Dr, Room 13C120
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
 
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
Relations
BioSample SAMN41151427
SRA SRX24423318

Supplementary file Size Download File type/resource
GSM8245392_HN_fHiC_008_33_NMU_1h_WT_ILC2_rep2.hic 383.7 Mb (ftp)(http) HIC
SRA Run SelectorHelp
Raw data are available in SRA

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