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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 20, 2024 |
| Title |
Brain, B-NHL+ CAR T cell therapy |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: Brain
cell type: Microglia, neuron, Oligodencrocytes
genotype: C57BL/6
treatment: B-NHL + CD19 CAR T cell therapy
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Mice were treated with B-NHL cells and 7 days later and NT or CD19 CAR T cells treatment. On day 10, mice were perfused with cold HBSS and brains were extracted and flash frozen. A small portion of Cortex tissue was excised from the CNS tissue and enriched for myeloid cells with modified Frankenstein’s protocol. Briefly, CNS tissue was homogenized in Nuclei EZ lysis buffer (Millipore Sigma) and upon incubation was filtere through 70µm filter. The suspension was centrifuged at 600g for 5 min at 4°C. The pellet was washed with nuclei wash and resuspension buffer (1x PBS, 1.0% BSA, 0.2 U/μl RNase Inhibitor) and centrifuged at 600g for5min at 4°C.Following this, Nuclei were stained for DAPI, NeuN and Olig 2 markers and sorted by Flow cytometry.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 1000 |
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| Description |
10x Genomics
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| Data processing |
The demultiplexing was carried out using in-built Illumina software on Next-seq 1000.
Barcode processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
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| Submission date |
Jan 24, 2023 |
| Last update date |
Feb 20, 2024 |
| Contact name |
Gianni Monaco |
| E-mail(s) |
mongianni1@gmail.com
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| Organization name |
Freiburg Medical Center
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| Street address |
Breisacher Straße
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| City |
Freiburg |
| ZIP/Postal code |
79106 |
| Country |
Germany |
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| Platform ID |
GPL32159 |
| Series (1) |
| GSE223647 |
Gene expression analysis at single cell level from the CNS of mice that recieved B-NHL and treated with either Non Transduced (NT) or CD19 Chimeric Antigen Receptor (CAR) T cells |
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| Relations |
| BioSample |
SAMN32897282 |
| SRA |
SRX19161073 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6969932_CAR_barcodes.tsv.gz |
46.3 Kb |
(ftp)(http) |
TSV |
| GSM6969932_CAR_features.tsv.gz |
226.2 Kb |
(ftp)(http) |
TSV |
| GSM6969932_CAR_matrix.mtx.gz |
34.7 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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