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| Status |
Public on Jun 15, 2024 |
| Title |
Analysis of chromosomal structual aberratons in NB-4 cell line |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
This Hi-C experiment was a part of a research which analyzed chromosomal structural aberrations in hematological malignancies. First, the author conducted comprehensive detection of fusion transcripts in RNA-seq data of DSMZ’s 99 cell lines, and then picked up cell lines with characteristic complex karyotype. NB-4 cell line is one of them, which shows characteristic fusion cluster in 8q24 region in the fusion detection step. This Hi-C experiment revealed amplifications of MYC, PVT1, and CCDC26 in 8q24 region. Additionally, several structural aberrations were found by scanning the whole genome.
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| Overall design |
in situ Hi-C of DSMZ’s NB-4 cell line with no treatment
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| Contributor(s) |
Kobayashi T, Watabe K, Motoko N |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jun 16, 2023 |
| Last update date |
Jun 15, 2024 |
| Contact name |
Tetsuko Kobayashi |
| Organization name |
Kyorin University
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| Street address |
Shimorenjaku5-4-1
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| City |
Mitaka-shi |
| State/province |
Tokyo |
| ZIP/Postal code |
181-8612 |
| Country |
Japan |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (1) |
| GSM7496018 |
in situ Hi-C of DSMZ’s NB-4 cell line with no stimulation |
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| Relations |
| BioProject |
PRJNA984680 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE235154_RAW.tar |
4.1 Gb |
(http)(custom) |
TAR (of BED, BEDPE, HIC, TBI, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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