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| Status |
Public on Nov 06, 2019 |
| Title |
InsituHiC_IMR90_OIS_CAPH2_KD3 |
| Sample type |
SRA |
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| Source name |
IMR90 cells
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| Organism |
Homo sapiens |
| Characteristics |
passage: 32-36
cell type: Lung fibroblasts
karyotype: Normal diploid
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| Treatment protocol |
pBABE-puro plasmids carrying H-rasV12 were used for retrovirus packaging, and virus infection was performed. H-rasV12-expressing cells were cultured in medium containing 1 µg/ml puromycin for 7 days to obtain OIS cells. pTRIPZ plasmids containing NCAPH2 shRNAs (#1, V3THS_326285; #2, V3THS_326286; #3, V3THS_326290, Dharmacon) were used for CAP-H2 knockdown. Lentivirus was prepared using ViraPower kit (Thermo Fisher Scientifc) according to the manufacturer’s protocol. Doxycycline (1μg/ml) was added to culture medium every 48 hours after lentiviral transfection for shRNA expression. OIS cells were further infected with lentivirus encoding one of the three shRNA constructs (#1, #2, and #3) against NCAPH2 and harvested 3 days after the lentivirus infection.
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| Growth protocol |
Normal diploid IMR90 human fibroblasts were cultured in DMEM medium supplemented with 10% FBS, 100 U/ml penicillin, 100 μg/ml streptomycin, 0.15% sodium bicarbonate, 2 mM L-glutamine, 1 mM sodium pyruvate, and 1 ´ MEM non-essential amino acids. BJ human fibroblasts were cultured in DMEM medium supplemented with 10% FBS, 100 U/ml penicillin, and 100 μg/ml streptomycin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
In situ Hi-C was performed as previously described (Rao et al., 2014, Cell)
Sequencing adapters were ligated using NEBNext Ultra Ligation module (New England Biolabs, Inc) on Dynabeads, and DNA was PCR-amplified for 8-14 cycles using NEBNext Q5 Hot Start HiFi PCR master Mix and NEBNext multiplex oligos (New England Biolabs, Inc).
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
76-bp paired reads were separately aligned to the human genome (hg19) using Bowtie2 (version 2.2.9) with iterative alignment strategy.
Redundant paired reads derived from a PCR bias, reads aligned to repetitive sequences, and reads with low mapping quality (MapQ < 30) were removed.
Contact matrices were generated at three resolutions such as 10, 40, 200 kb. The entire human genome was divided into 10, 40, 200 kb sections. A raw contact matrix was first constructed by counting paired reads assigned to two genomic sections. Note that reads belong to MboI fragments.
Reads potentially derived from self-ligation and undigested products were also discarded.
Hi-C biases in contact maps were corrected using the ICE method. The ICE normalization was repeated 30 times.
Genome_build: hg19
Supplementary_files_format_and_content: tab-deliminated text files of normalized scores. First row and column indicate the location of the genome in following format, "<chromosome name>:<start position>:<end position>"
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| Submission date |
Aug 13, 2018 |
| Last update date |
Nov 07, 2019 |
| Contact name |
Hideki Tanizawa |
| E-mail(s) |
hidekit@uoregon.edu
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| Organization name |
University of Oregon
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| Department |
Institute of Molecular Biology
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| Street address |
1370 Franklin Blvd
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| City |
Eugene |
| State/province |
OR |
| ZIP/Postal code |
97403 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE118494 |
Involvement of Condensin in Cellular Senescence through Gene Regulation and Compartmental Reorganization |
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| Relations |
| BioSample |
SAMN09828217 |
| SRA |
SRX4549829 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3330973_InsituHiC_IMR90_OIS_CAPH2_KD3_Raw_matrices.tar.gz |
23.4 Mb |
(ftp)(http) |
TAR |
| GSM3330973_InsituHiC_IMR90_OIS_CAPH2_KD3_normalized_matrices.tar.gz |
161.2 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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