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| Status |
Public on Nov 12, 2023 |
| Title |
Bone marrow plasma cells |
| Sample type |
SRA |
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| Source name |
bone marrow
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| Organism |
Homo sapiens |
| Characteristics |
cell type: plasma cells
tissue: bone marrow
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| Extracted molecule |
total RNA |
| Extraction protocol |
Human plasma cells were sorted as CD138+CD38hi into ice-cold 0.5% bovine serum albumin (BSA) in PBS.
Cells were processed through the 10x Chromium Single Cell 3′ v2 Library Kit (10× Genomics), according to the manufacturer’s protocol. The channel was loaded with 10,000 cells yielding 6747 single cells for analysis. The cells were then partitioned into gel beads in emulsion in the instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, shearing, and 5′-adapter and sample index attachment.
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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 |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Cell Ranger v5.0.0 was used to create raw read FASTQ files. Genewise reads counts were generated with Cell Ranger v7.0.0 using a custom reference made with the newly published human T2T-CHM13 reference assembly and a custom GTF file specific to human plasma cell usage.
Assembly: T2T-CHM13
Supplementary files format and content: Standard 10x output consisting of tab-separated text files and with read counts in matrix-market format.
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| Submission date |
Apr 18, 2023 |
| Last update date |
Nov 12, 2023 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
smyth@wehi.edu.au
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| Phone |
(+61 3) 9345 2326
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| Fax |
(+61 3) 9347 0852
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| URL |
http://www.wehi.edu.au
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| Organization name |
Walter and Eliza Hall Institute of Medical Research
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| Department |
Bioinformatics
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| Lab |
Smyth
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| Street address |
1G Royal Pde
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| City |
Parkville |
| State/province |
Vic |
| ZIP/Postal code |
3052 |
| Country |
Australia |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE229957 |
Gene expression profile at single cell level of plasma cells (PCs) from human bone marrow |
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| Relations |
| BioSample |
SAMN34234236 |
| SRA |
SRX20001597 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7181915_barcodes.tsv.gz |
36.2 Kb |
(ftp)(http) |
TSV |
| GSM7181915_features.tsv.gz |
189.9 Kb |
(ftp)(http) |
TSV |
| GSM7181915_matrix.mtx.gz |
41.3 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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