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| Status |
Public on May 24, 2018 |
| Title |
Single cell RNA sequencing of multiple myeloma II |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To investigate the relationship between genetic and transcriptional heterogeneity in a context of cancer progression, we devised a computational approach called HoneyBADGER to identify copy number variation and loss-of-heterozygosity in individual cells from single-cell RNA-sequencing data. By combining allele frequency and expression magnitude deviations, HoneyBADGER is able to infer the presence of subclone-specific alterations in individual cells and reconstruct subclonal architecture. Also HoneyBADGER to analyze single cells from a progressive multiple myeloma (MM) patient to identify major genetic subclones that exhibit distinct transcriptional signatures relevant to cancer progression.
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| Overall design |
We performed single cell RNA sequencing (RNA-seq) for multiple myeloma from the bone marrow and/or extramedullary sites from 3 patients. Data contain 173 and 1,339 single-cell RNA-seq from Fluidigm C1 and 10x Genomics respectively.
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| Contributor(s) |
Fan J, Kharchenko P, Ryu D, Lee H, Kim K, Park W |
| Citation(s) |
29898899, 31558476 |
| Submission date |
Feb 12, 2018 |
| Last update date |
Oct 17, 2019 |
| Contact name |
Daeun Ryu |
| E-mail(s) |
daeun.dawn.ryu@gmail.com
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| Organization name |
Samsung Genome Institute
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| Street address |
81, Irwon-ro
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| City |
Seoul |
| ZIP/Postal code |
06351 |
| Country |
South Korea |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (174)
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| Relations |
| BioProject |
PRJNA433864 |
| SRA |
SRP132719 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE110499_GEO_processed_MM_10X_raw_UMI_count_martix.txt.gz |
3.3 Mb |
(ftp)(http) |
TXT |
| GSE110499_GEO_processed_MM_raw_TPM_matrix.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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