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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 12, 2018 |
| Title |
male_C57BL6_FirreKO_and_Cast_WT_HiC_Biological_Rep1_Technical_Rep2 |
| Sample type |
SRA |
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| Source name |
Mouse Embryonic Fibroblasts
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| Organism |
Mus musculus |
| Characteristics |
genotype: Allelic_FirreKO
cell type: Mouse Embryonic Fibroblasts
Sex: Male
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C libraries were generated with the in-situ ligation protocol using the HindIII restriction enzyme. Briefly, ~25 million cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Then, the chromatin was digested with HindIII, end-labelled with biotin-14-dCTP, and in-situ ligation was performed. Following phenol-chloroform extraction, the biotin was removed from unligated ends, and the DNA was sheared by using a Covaris S220 instrument. After A-tailing, biotin pull-down and adapter ligation, paired-end sequencing was performed on a HiSeq instrument. Each Hi-C library was generated in at least two biological replicates from MEFs prepared from at least two distinct mouse embryos.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Hi-C
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| Data processing |
Hi-C mapping, filtering, correction and binning was performed with the HiC-Pro software v2.7.8. The reads were mapped to the mm9 mouse reference genome. For allele-specific Hi-C analysis, a high quality SNP list for the C57BL6NJ and CastEiJ genomes was generated by using the mm9 annotation from the Mouse Sanger Database, using the HiC-Pro “extract_snps.py” tool. Next, C57BL6NJ/CastEiJ SNP-masked mm9 reference genome was generated using the bedtools “maskfasta” tool. Then, allele-specific Hi-C data was analyzed using the HiC-Pro “ALLELE_SPECIFIC_SNP” configuration option. There was a high correlation among the Hi-C biological replicates, indicating the high quality and reproducibility of the datasets. Therefore, we pooled all biological replicates for each condition and mapped, filtered, corrected and binned them as a single Hi-C dataset, and used the pooled datasets for all subsequent analyses. The read-depth achieved for each pooled Hi-C dataset supports the generation of genome-wide contact maps at as low as 40kb resolution.
For the Hi-C analysis of endogenous Firre KO with ectopic Firre cDNA insertion MEFs, the Hi-C reads were mapped to a custom mm9 genome with an extra chromosome consisting of the insertion cassette (TRE element, CMV promoter, Firre cDNA and polyA terminator (). Then, “inter-chromosomal interactions” between the Firre custom chromosome and all the mouse chromosomes were plotted in the DOX- and DOX+ Hi-C datasets. The regions which displayed consistent “interactions” with the Firre custom chromosome in DOX- and DOX+ samples were determined as Firre cDNA insertion sites.
Genome_build: mm9
Supplementary_files_format_and_content: Processed, iterative corrected sparse Hi-C matrix
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| Submission date |
May 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Rasim Barutcu |
| Organization name |
ScitoVation
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| Street address |
6 Davis Drive
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE98632 |
A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus |
| GSE104367 |
A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus [HiC_MEF] |
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| Relations |
| BioSample |
SAMN06909634 |
| SRA |
SRX3241601 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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