|
| Status |
Public on Sep 14, 2022 |
| Title |
MM043 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: bortezomib-melphalan-prednisolone
tissue: Bone marrow
disease state: Multiple myeloma
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bone marrow aspirate samples were collected at baseline prior to the induction treatment of VMP or VTD. BM aspirates were subjected to a Ficolle-Paque PLUS gradient, and isolated mononuclear cells were cryopreserved in freezing medium before the experiments.
The single-cell library preparation relied on a commercially available droplet method, the 10x Genomic Chromium System (10x Genomic Inc., San Francisco, CA), with 10x Genomics Single Cell 3’ v3 Reagent kit according to the manufacturer’s protocol. In brief, dissociated cells were counted by hemocytometer (ThermoFisher) and 16,000 cells per sample were added to each channel. The cells were then partitioned into gel beads in emulsion (GEMs) in the Chromium instrument, where cell lysis and barcoded reverse transcription of RNA occurred. cDNA was synthesized and amplified for 14 cycles. cDNA clean-up was performed using a SPRIselect Reagent Kit (Beckman Coulter, Brea, CA). 50 ng of the amplified cDNA were used for each sample to construct indexed sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The sequenced data were processed into expression matrices with the Cell Ranger Single Cell software suite v3.0.1 by 10x Genomics.
Raw base-call files from HiSeq2500 sequencer were demultiplexed into library-specific FASTQ files using Cell Ranger mkfastq option.
Sequencing reads were mapped to the GRCh38 (version 3.0.0) reference
Cell barcodes and unique molecular identifiers underwent filtering and correction. Reads associated with the retained barcodes were quantified using Cell Ranger count option and used to build a transcript count table.
Genome_build: GRCh38
Supplementary_files_format_and_content: h5 format: Contains the per molecule read information from Cell Ranger. The instructions to read the matrix in hdf5 format can be found here: https://support.10xgenomics.com/single-cell/software/pipelines/latest/advanced/h5_matrices
|
| |
|
| Submission date |
Nov 23, 2021 |
| Last update date |
Sep 17, 2022 |
| Contact name |
SeungHyun Jung |
| E-mail(s) |
hyun@catholic.ac.kr
|
| Phone |
82-2-2258-7509
|
| Organization name |
Catholic University of Korea
|
| Department |
Department of Biochemistry
|
| Street address |
catholic university, medical college, banpo-dong
|
| City |
seoul |
| State/province |
seoul |
| ZIP/Postal code |
06591 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE189460 |
Identification of genes associated with bortezomib-based treatment in multiple myeloma patients through bone marrow single-cell RNA-Seq |
|
| Relations |
| BioSample |
SAMN23415406 |
| SRA |
SRX13213183 |
