HCA Data Explorer

Single cell RNA sequencing of multiple myeloma II

Updated November 15, 2021

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.

Daeun RyuSamsung Genome Institutedaeun.dawn.ryu@gmail.com
Daeun Ryu (Experimental Scientist)1
1Samsung Genome Institute
Hernandez Karina
Nguy Beagan
Parisa Nejad

To reference this project, please use the following link:

https://explore.data.humancellatlas.dev.clevercanary.com/projects/0c3b7785-f74d-4091-8616-a68757e4c2a8

Supplementary links are provided by contributors and represent items such as additional data which can’t be hosted here; code that was used to analyze this data; or tools and visualizations associated with this specific dataset.

1.ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110499/suppl/GSE110499_GEO_processed_MM_10X_raw_UMI_count_martix.txt.gz,ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110499/suppl/GSE110499_GEO_processed_MM_raw_TPM_matrix.txt.gz
INSDC Project Accessions:GEO Series Accessions:

Atlas

None

Analysis Portals

None

Project Label

HumanBoneMarrowMyeloma

Species

Homo sapiens

Sample Type

specimens

Anatomical Entity

hematopoietic system

Organ Part

2 organ parts

Selected Cell Types

plasma cell

Disease Status (Specimen)

plasma cell myeloma

Disease Status (Donor)

plasma cell myeloma

Development Stage

human adult stage

Library Construction Method

2 library construction methods

Nucleic Acid Source

single cell

Paired End

false, true

Analysis Protocol

MultiSampleSmartSeq2_v2.2.6, SmartSeq2SingleSample_v5.1.5, optimus_post_processing_v1.0.0, optimus_v4.2.3

File Format

5 file formats

Cell Count Estimate

1.5k

Donor Count

3
bai173 file(s)bam174 file(s)fastq.gz352 file(s)loom3 file(s)txt.gz2 file(s)