NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2587501 Query DataSets for GSM2587501
Status Public on Nov 13, 2017
Title 9E HiC rep 1
Sample type SRA
 
Source name 9E HiC
Organisms Homo sapiens; Human papillomavirus 16
Characteristics cell type: 9E cells
Treatment protocol All cells except Akata-Zta were untreated. 5 million cells per experiment were fixed for in situ Hi-C as previously described (Rao et al., 2014). Akata-Zta cells were pretreated with 200 μM acyclovir for 1 hour before reactivation of the lytic cycle with 500 ng/mL doxycycline. After 1 day, cells were magnetically sorted using LNGFR Microbeads and LS columns (Miltenyi Biotech). 5 million cells each of LGNFR+ and LGNFR- were fixed for in situ Hi-C as previously described (Rao et al. 2014)
Growth protocol EBV-positive Daudi, KemIII, RaeI, and Raji cells were maintained under standard conditions (Phan et al., 2016). K562 (C. B. Lozzio and B. B. Lozzio, 1975), EBV- and KSHV-positive BC-1 (Cesarman et al., 1995) and EBV-positive Namalwa (Klein et al., 1972) cells were maintained in RPMI-1640 with 25 mM HEPES and 2 g/L NaHCO3 supplemented with 10% (v/v) fetal bovine serum (Invitrogen) in 5% CO2 at 37 °C. EBV-positive Akata-Zta cells (Ramasubramanyan et al., 2015) were maintained in RPMI-1640 with 25 mM HEPES and 2 g/L NaHCO3 supplemented with 10% (v/v) Tet System Approved fetal bovine serum (Clontech). The HPV16-positive 20863 (Jeon et al., 1995) and HPV31-positive 9E (De Geest et al., 1993) keratinocyte cell lines were grown in F-medium, 3:1 (v/v) F-12-DMEM, 5% fetal bovine serum, 400 ng/ml hydrocortisone, 5 µg/ml insulin, 8.4 ng/ml cholera toxin, 10 ng/ml epidermal growth factor, 24 µg/ml adenine, 100 U/ml penicillin, and 100 µg/ml streptomycin, in the presence of irradiated 3T3-J2 feeder cells, as described previously (Chapman et al., 2014). Irradiated feeder cells were removed by versene treatment before the cells were harvested.
Extracted molecule genomic DNA
Extraction protocol In situ Hi-C was performed with 5 million cells per experiment and restriction enzyme MboI as described (Rao et al., 2014) with slight modifications. After end-repair and washes, Dynabeads (Thermo Fisher Scientific) with bound DNA were resuspended in 10 mM Tris, 0.1 mM EDTA pH 8.0 and transferred to new tubes.
Sequencing libraries were created from bound DNA using the Ovation Ultralow Library System V2 kit (NuGEN) with one modification. After adapter ligation, because DNA is still attached to the beads, water instead of SPRI beads was added to the reaction. DNA bound to the beads was purified with a magnet, washed, and the beads were resuspended in 10 mM Tris, 0.1 mM EDTA pH 8.0. After library amplification, SPRI beads were added as directed to purify the amplified DNA.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Data processing library strategy: HiC-seq
General HiC processing: Paired reads were aligned to combined human/viral reference genomes with HiCUP version 0.5.0 using default parameters (Wingett et al., 2015) to generate a set of interactions. We used the human hg19 sequence merged with the EBV NC_007605.1, KSHV NC_009333.1, HPV16 NC_001526.2, or HPV31 J04353.1 sequence. Only alignments with mapq scores equal to or greater than 30 were retained.
Chromosome-resolution heatmaps of interactions were determined from the HiCUP-filtered interchromosomal Hi-C interactions in sam format. Expected interactions were calculated using the following equation for each chromosome pair, where chrA represents the number of single end interchromosomal reads containing chrA, chrB represents the number of single end interchromosomal reads containing chrB, totalPairs represents the total number of interchromosomal paired end reads, and all represents the total number of interchromosomal single end reads, which is equal to 2 x totalPairs: (((chrA/all)*(chrB/(all-chrA)))+((chrB/all)*(chrA/(all-chrB)))) * total_pairs.
Lamin association analysis: The set of lamin interacting domains from Tig3 cells (Guelen et al., 2008) was downloaded from the UCSC genome browser (Kent et al., 2002). Hi-C interactions identified by HiCUP were processed into a format readable by the HiTC package (Servant, 2015) using 1 Mb bins for the human genome and 1 kb bins for the viral genome. We performed further analyses on these interaction matrices in R (R Core Team, 2016). First a full interaction matrix for all autosomes was constructed. Next, for each bin, the mean of interaction counts with LAD bins was calculated as was the mean of interaction counts with non-LAD bins. Correlations were then performed across all autosomal bins with the LAD mean vector and the non-LAD mean vector. A logistic regression was performed on the LAD and non-LAD correlation values estimate the probability with which each genome region would interact with lamin. Next, we calculated the probability that each viral bin interacted with the lamin by applying the logistic regression model of the autosomal LAD correlations to the viral interaction data.
Genome_build: human hg19 sequence merged with the EBV NC_007605.1, KSHV NC_009333.1, HPV16 NC_001526.2, or HPV31 J04353.1 sequence
Supplementary_files_format_and_content: Chromsome-resolution heatmap generation results in two plain text files *interchrom_raw_counts_label.txt and *obs_exp_log2_label.txt. The *interchrom_raw_counts_label.txt contains a labeled 26 x 26 matrix for the raw counts of interchromosomal interactions between whole chromosomes. The *obs_exp_log2_label.txt file contains the same labeled 26 x 26 matrix, with raw interchromosomal counts normalized as described above.
Supplementary_files_format_and_content: Lamin association analysis results in plain text files ending in *allCounts.txt, which contains three columns, the first two are individual genomic bins and the third column is the number of interactions between those two bins.
 
Submission date Apr 24, 2017
Last update date May 15, 2019
Contact name JJ Miranda
E-mail(s) jmiranda@barnard.edu
Organization name Barnard College, Columbia University
Street address 3009 Broadway
City New York
ZIP/Postal code 10027
Country USA
 
Platform ID GPL22767
Series (2)
GSE98120 The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation [HiC-seq]
GSE98123 The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation
Relations
BioSample SAMN06824403
SRA SRX2755224

Supplementary file Size Download File type/resource
GSM2587501_9E_rep1_h1000000_v1000_allCounts.txt.gz 19.7 Mb (ftp)(http) TXT
GSM2587501_9E_rep1_interchrom_raw_counts_label.txt.gz 1.7 Kb (ftp)(http) TXT
GSM2587501_9E_rep1_obs_exp_log2_label.txt.gz 1.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap