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| Status |
Public on Sep 27, 2023 |
| Title |
MPAL Patient 1, Diagnosis |
| Sample type |
SRA |
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| Source name |
bone marrow
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| Organism |
Homo sapiens |
| Characteristics |
individual: patient 1
tissue: bone marrow
sample type: diagnosis
cell type: Bone marrow blast and immune cells
disease state: MPAL
diagnosis subtype: B/My MPAL
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| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen bone marrow samples were obtained from Aflac Cancer and Blood disorder center from Children’s Healthcare of Atlanta Pediatric Biorepository.The frozen BM were thawed viably using standardized protocol. Briefly the cells were thawed quickly (37C for ~2 minutes till a small ice crystal remains), and warm complete medium (RPMI1640, 5% heat inactivated FBS, 1x Penicillin. Streptomycin) was added gradually. The cells were pelleted (380g, RT, 5min), and washed one more time with complete medium, which was followed by one more wash with PBS containing BSA (0.04 to 1.0%). For cell multiplexing, cells were labelled with specific anti-human TotalSeq-B Hashtag antibodies (Biolegend) according to manufacturer’s protocol. The cells were resuspended in cell staining buffer (Biolegend) or PBS with1% BSA to get an optimal cell concentration of 700-1200 cells/µl. The single cell suspensions were then proceeded using 10x Genomics single cell assay protocols.
The single cell RNA-seq libraries were prepared using the Chromium single cell 3’v3 and 3’ v3.1 reagent kits (10x Genomics). The libraries were quantified using Qubit (Thermo Fisher Scientific) and quality was checked using Bioanalyzer HS DNA chips (Agilent). Sequencing was performed using the massively parallel sequencing NextSeq 500 and Novaseq S4 platforms (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
10X Genomics
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| Data processing |
Raw scRNA-seq data was demultiplexed, aligned to human reference genome, and processed for single cell gene counting using the Cell Ranger Software from 10x Genomics (v7.0.0).
Assembly: hg38
Supplementary files format and content: Tab separated values files and matrix files
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| Submission date |
Jul 03, 2023 |
| Last update date |
Sep 27, 2023 |
| Contact name |
Hope Mumme |
| E-mail(s) |
hmumme@emory.edu
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| Organization name |
Emory University
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| Street address |
1760 Haygood Dr NE
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| City |
Atlanta |
| ZIP/Postal code |
30322 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE236351 |
Single-cell RNA sequencing distinctly characterizes the wide heterogeneity in pediatric mixed phenotype acute leukemia |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM7528325_M1_barcodes.tsv.gz |
19.8 Kb |
(ftp)(http) |
TSV |
| GSM7528325_M1_features.tsv.gz |
126.2 Kb |
(ftp)(http) |
TSV |
| GSM7528325_M1_matrix.mtx.gz |
27.2 Mb |
(ftp)(http) |
MTX |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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