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Sample GSM7040844 Query DataSets for GSM7040844
Status Public on Sep 21, 2023
Title Patient_P1608_Pre_Treatment_scRNA-seq
Sample type SRA
 
Source name Primary CD138+ MM cells
Organism Homo sapiens
Characteristics patient number: P1608
time point: Pre
cell type: Primary CD138+ MM cells
library preparation: 10X Genomics Single Cell RNAseq v2 Chemistry
Growth protocol Primary CD138+ MM cells were obtained from the BM aspirates of MM patients at the time of diagnostic procedure, using positive selection with CD138 microbeads (Miltenyi Biotech, Auburn, CA) and accordingly to manufacturer’s instructions. CD138+ fractions were subsequently analyzed by flow cytometry in order to confirm the sample’s purity. HEK293T cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% FBS, 100 U/mL penicillin and 100 g/mL streptomycin. All of the listed cells above were cultured at 37°C and 5% CO2.
Extracted molecule polyA RNA
Extraction protocol Single-cell library preparation for RNA-sequencing primary MM cells were processed according to 10X Genomics reagent Kits User Guide (CG00052 v2 Chemistry). Cells were partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs) using 10X GemCode Technology. Primers containing (i) an Illumina R1 sequence, (ii) a 16 bp 10x barcode, (iii) a 10 bp Unique Molecular Identifier (UMI) and (iv) a poly-dT primer sequence were incubated with partitioned cells resulting in barcoded, full-length cDNA from poly-adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents/primers, then cDNA was amplified by PCR. Enzymatic Fragmentation and Size Selection was used to optimize cDNA amplicon size prior to library construction. R1 (read 1 primer sequence) were added during GEM incubation, whereas P5, P7, a sample index (i7), and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation and PCR.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing All raw FASTQs reads were aligned against the human reference genome GRCh38 with default parameters.
Assembly: Human referene genome GRCh38
Supplementary files format and content: Filtered feature - barcode HDF5 file output from CellRanger pipeline
 
Submission date Feb 13, 2023
Last update date Sep 21, 2023
Contact name Nizar Bahlis
E-mail(s) nbahlis@ucalgary.ca
Phone 403-220-2801
Organization name University of Calgary
Department Divisions of Hematology and Oncology
Street address 3330 Hospital Dr NW HMRB328
City Calgary
State/province Alberta
ZIP/Postal code T2N4N1
Country Canada
 
Platform ID GPL18573
Series (2)
GSE199359 scRNAseq Datasets Supporting Integrated Epigenetic and Transcriptional Single-Cell Analysis of t(11;14) Multiple Myeloma and Its BCL2 Dependency
GSE199373 Integrated Epigenetic and Transcriptional Single-Cell Analysis of t(11;14) Multiple Myeloma and Its BCL2 Dependency
Relations
BioSample SAMN33271101
SRA SRX19353445

Supplementary file Size Download File type/resource
GSM7040844_P1608_Pre_filtered_feature_bc_matrix.h5 22.4 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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