Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species
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PRJNA415945

PRJNA415945: Single cell RNA sequencing of multiple myeloma I

Source: NCBI / GSE106218
Submission Date: Oct 26 2017
Release Date: Oct 17 2019
Update Date: Oct 17 2019

Summary: To understand molecular events associated with myeloma progression, we applied single-cell RNA sequencing to myeloma cells in the bone marrow and extramedullary sites. Transcriptome analysis, at single cell level, demonstrates that proliferation and alterations in antigen presentation are associated with myeloma progression whereas NF-kB pathway activation has an anti-correlation. While these alterations are prominent in most of the extramedullary myeloma cells, some myeloma cells in the bone marrow show gene expression signatures resembling extramedullary cells even when the myeloma cells were taken at stable disease. Altogether single-cell transcriptome analysis reveals both common transcriptional programs and heterogeneity turned on during myeloma progression.

Overall Design: We performed single cell RNA sequencing (RNA-seq) for multiple myeloma from the bone marrow and/or extramedullary sites from 10 patients. Additional bulk RNA sequencing was performed with CD138-negative non-myeloma populations from the same patients. Data contain 477 single-cell RNA-seq and 11 bulk RNA-seq.

GEN Datasets:
GEND000210 GEND000211
Strategy:
Species:
Tissue:
Healthy Condition:
Cell Type:
Protocol
Growth Protocol: -
Treatment Protocol: Bortezomib treatment
Extract Protocol: Plasma cell were purified using EasySep(®) CD138 Positive Selection kit before loading to integrated fluidic circuit (IFC) chip. Each suspension was loaded to 5-10um IFC for mRNA sequencing chip then cDNA synthesis and amplification were performed with SMARTer Ultra Low RNA Kit (Clontech) in the C1TM Single-Cell Auto Prep System (Fluidigm). Two types of external sequence, 1,4,7 ArrayControl TM RNA Spikes and ERCC RNA Spike-In Control Mix (ThermoFisher) were added to the lysis mix for validation of array and batch effect. All of amplified cDNAs were quantified and qualified by the Qubit® 2.0 Fluorometer (Life Technologies) and 2100 Bioanalyzer (Agilent Technologies).; Plasma cells were purified using EasySep(®) CD138 Positive Selection kit before loading to integrated fluidic circuit (IFC) chip. Each suspension was loaded to 5-10um IFC for mRNA sequencing chip then cDNA synthesis and amplification were performed with SMARTer Ultra Low RNA Kit (Clontech) in the C1TM Single-Cell Auto Prep System (Fluidigm). Two types of external sequence, 1,4,7 ArrayControl TM RNA Spikes and ERCC RNA Spike-In Control Mix (ThermoFisher) were added to the lysis mix for validation of array and batch effect. All of amplified cDNAs were quantified and qualified by the Qubit® 2.0 Fluorometer (Life Technologies) and 2100 Bioanalyzer (Agilent Technologies).
Library Construction Protocol: Whole-transcriptome sequencing libraries were generated for the RNAs from CD138-negative cell fractions using a TruSeq RNA Sample Preparation v2 Kit (Illumina).; Sequencing libraries were constructed using amplified cDNAs with the Nextera XT DNA Sample Prep Kit (Illumina) and sequenced using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS Kit (Illumina).
Sequencing
Molecule Type: poly(A)+ RNA; rRNA- RNA
Library Source:
Library Layout: PAIRED
Library Strand: Forward; -
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 2500
Strand-Specific: Specific; Unspecific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate
Publications
Alterations in the Transcriptional Programs of Myeloma Cells and the Microenvironment during Extramedullary Progression Affect Proliferation and Immune Evasion.
Clinical cancer research : an official journal of the American Association for Cancer Research . 2019-09-26 [PMID: 31558476]