|
| Status |
Public on Apr 09, 2024 |
| Title |
passage 6 spleen untreated, 1 |
| Sample type |
SRA |
| |
|
| Source name |
spleen
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
tissue: spleen
cell type: primary human mantle cell lymphoma cells and murine splenocytes
treatment: untreated
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single splenocytes were isolated using the 10X Genomics 5' Capture Immune Profiling kit. For samples with less than 75% viability, the Miltenyi dead cell removal kit was used.
Gene expression and immune receptor libraries were constructed according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Mus musculus/Homo Sapiens xenograft
10x Genomics
|
| Data processing |
Cell barcode/gene count matrices were generated using Cellranger v 6.1.2. The reads were aligned to the combined GRCh38/mm10 reference.
Human cells were selected using the sample_barcodes.csv file generated by Cellranger.
Low quality cells were identified by low feature counts (more than 2 median absolute deviations less than the median for the sample) or high percent of mitochondrial reads (more than 2 median absolute deviations greater than the median for the sample) and filtered out.
Doubletfinder was used to predict and remove high-likelihood doublet events.
Dimension reduction was performed using PCA and UMAP algorithms implemented within monocle3.
Clustering was performed using the louvain, leiden and partitioning algorithms as implemented in monocle3.
Assembly: GRCh38/mm10
Supplementary files format and content: XX_barcodes.tsv.gz: tab delimited file containing filtered cell barcodes generated by Cellranger.
Supplementary files format and content: XX_features.tsv.gz: tab delimited file containing gene identifiers from the GRCh38/mm10 reference
Supplementary files format and content: XX_matrix.mtx.gz: Sparse matrix containing gene counts per cell barcode.
Supplementary files format and content: XX_sample_barcodes.csv: comma delimited file with cell barcodes and genome identified by Cellranger.
|
| |
|
| Submission date |
Apr 12, 2023 |
| Last update date |
Apr 09, 2024 |
| Contact name |
Bradley Wayne Blaser |
| E-mail(s) |
bradley.blaser@osumc.edu
|
| Organization name |
Ohio State University
|
| Department |
Comprehensive Cancer Center
|
| Lab |
Blaser Lab
|
| Street address |
400 W 12th Ave
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL25526 |
| Series (1) |
| GSE229517 |
Resistance to PRMT5-targeted therapy in mantle cell lymphoma |
|
| Relations |
| SRA |
SRX19944404 |
| BioSample |
SAMN34156568 |
