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| Status |
Public on Oct 08, 2022 |
| Title |
UPN3550_HiC |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain
cell line: UPN3550
cell type: medulloblastoma cells
genotype: wt
treatment: no
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| Treatment protocol |
no treatment
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| Growth protocol |
UPN3550 cells were isolated from a group 4 MB patient's primary tumor tissue, in DMEM/F12 with 10% FBS, 2 mM L-glutamine and 1% penicillin/streptomycin. MB-004 cells were cultured in neurobasal medium (Sigma; SCM003) with 2% B-27, 1 mg/ml heparin, 2 mM L-glutamine and 1% penicillin/streptomycin, 25 ng/ml FGF and 25 ng/ml EGF at 37℃ in an atmosphere of 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Five million cells for each cell line were cross-linked with 1% formaldehyde for 10 mins at room temperature and then then quenched with 0.2M Glycine. Cell pellets were washed with cold PBS and lysed with lysis buffer to get nuclei pellets.
MB004 (G3 MB) and UPN3550 (G4 MB) cells were processed for Hi-C library construction using the Arima Hi-C Kit following the manual (Arima Genomics). Briefly, nuclei were permeabilized and in situ digested. KAPA Hyper Prep kit was used for library amplification (KAPA, KK2802).
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Hi-C libraries were sequenced 2×150bp on a NovaSeq 6000 instrument (Illumina).
Reads were processed using Juicer, aligning to reference genome hg38 to generate Hi-C contact matrices (.hic files).
Contact matrices were visualized using Juicebox.
Assembly: Hg38
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| Submission date |
Apr 19, 2022 |
| Last update date |
Oct 10, 2022 |
| Contact name |
Zaili Luo |
| Organization name |
CCHMC
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| Lab |
Richard Lu
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| Street address |
3333 Burnet Ave.
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| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE198565 |
Single cell transcriptional and chromatin accessibility profiling identify the cellular heterogeneity of human medulloblastoma |
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| Relations |
| BioSample |
SAMN27646296 |
| SRA |
SRX14924073 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6050304_UPN3550_inter_30.hic |
4.1 Gb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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