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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 15, 2016 |
| Title |
DS23114 |
| Sample type |
SRA |
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| Source name |
immortalized cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: NCIH460B
cell type: Human large cell lung carcinoma
restriction enzyme: HindIII
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| Growth protocol |
This is an adherent cell line and was passaged according to ATCC protocols, except that cells were dispersed using Accutase (Sigma A-6964) rather than Trypsin
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C experiment were conducted according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).)
Libraries were prepared according to Illumina's protocol for Truseq library construction, with the following modifications: Volumes and primers were scaled down to accommodate low input material.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Basecalls performed using CASAVA
HiC data sets were aligned against hg19, binned and normalized using the methods described in "The Hitchhiker's guide to Hi-C analysis: practical guidelines", Methods, 2015, Lajoie et.al.
Binning, normalization and further downstream analysis of the data was done using the method in "Structural organization of the inactive X chromosome in the mouse", Nature, 2016, by Giorgetti et. Al
Genome_build: hg19
Supplementary_files_format_and_content: tar archive containing raw and normalized interactions
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| Submission date |
Dec 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Job Dekker |
| Organization name |
UMass Medical School
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| Department |
Program in Systems Biology
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| Lab |
Dekker Labaratory
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| Street address |
368 Plantation Street
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| City |
Worcester |
| State/province |
Massachusetts |
| ZIP/Postal code |
01605 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE92390 |
HiC of selected non-small cell lung carcinoma cell lines |
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| Relations |
| BioSample |
SAMN06141586 |
| SRA |
SRX2422733 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2428901_matrix_NCIH460B.tar.gz |
1.3 Gb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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