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| Status |
Public on Apr 05, 2023 |
| Title |
MQpool1-GEX |
| Sample type |
SRA |
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| Source name |
PBMC
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| Organism |
Homo sapiens |
| Characteristics |
cell type: PBMC
cell type (sorted): CD45+CD19-CD3+CD56- cells
disease state: NSCLC
treatment: pre-treatment and on-treatment at 3, 6, 9 weeks
library type: mRNA
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single live CD45+CD19–CD3+CD56– cells were enriched from cryopreserved PBMC samples obtained pre-treatment and on-treatment at 3, 6, 9 weeks by flow cytometry sorting using a BD FACSAria II (BD Biosciences).
Cells were counted, hashed with TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253 and TotalSeq-C0254 anti-human antibodies, BioLegend) and pooled into 2 separate batchs (MQpool1, MQpool2).
The pooled cells were then counted again and immediately loaded onto the chromium chip G using the standard protocol for the Chromium single-cell 5’ kit v2 (10x Genomics, Inc).
Following the final bead purification, all three libraries were pooled as 80% mRNA library, 10% ADT library and 10% HTO library before sequencing.
scRNA/VDJ-seq (5'GEX, VDJ, HTO)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
5' mRNA library
5'RNA
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
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| Data processing |
Raw sequence data demultiplexing, barcode processing, alignment (GRCh38) and filtering for true cells were performed using the Cell Ranger Single-Cell Software Suite (v6.0.0)
Sample demultiplexing from hashtag feature barcoding (TotalSeq-C antibodies, BioLegend), subsequent filtering for high quality cells, and downstream analyses were performed using Seurat (v4)
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_contig_annotations.csv
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| Submission date |
Sep 21, 2022 |
| Last update date |
Apr 05, 2023 |
| Contact name |
Mark D Long |
| E-mail(s) |
[email protected]
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| Organization name |
Roswell Park Comprehensive Cancer Center
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| Department |
Bioinformatics & Biostatistics
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| Street address |
Elm & Carlton Streets
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| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14263 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE213902 |
The utility of circulating CX3CR1+ CD8+ T cells as a predictive correlate of response to chemo-immunotherapy in patients with non-small cell lung cancer |
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| Relations |
| BioSample |
SAMN30953988 |
| SRA |
SRX17663406 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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