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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 19, 2024 |
| Title |
10-weeks TCR |
| Sample type |
SRA |
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| Source name |
Pancreas
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| Organism |
Mus musculus |
| Characteristics |
tissue: Pancreas
cell type: T cells
genotype: NOD/ShiLtJ
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| Extracted molecule |
total RNA |
| Extraction protocol |
NOD mice were euthanized by CO2 asphyxiation and immediately dissected for pancreas perfusion and individual islet picking. Pancreas perfusion was performed under a dissecting microscope. The pancreatic duct was clamped using surgical clamps and 3 ml of 600 U/ml Collagenase IV (Gibco) dissolved in HBSS (Gibco) was injected using a 30G needle. Perfused pancreata were harvested and incubated at 37°C for 30 min. After the incubation, HBSS with R10 was added to quench collagenase. After washing twice with HBSS+R10, the tissue was plated on a 10 cm plate, individual islets were picked using a micropipettor. Islets were then incubated in dissociation buffer (Gibco), centrifuged, and resuspended in the staining mix (1:500 dilution of anti-Thy1.2-BV605 + 1:500 dilution of Live/Dead-APC-Cy7, and 1:100 dilution of cell hashing TotalSeq antibodies (Biolegend)). After staining, the cells were resuspended in PBS+0.04% BSA (Millipore Sigma) and sorted on BD FACS Aria III sorter. After sorting the cells, they were counted and processed for scRNAseq.
Cells were processing using 10x 5’ single cell gene expression kit v3 in a Chromium controller according to the manufacturer’s protocols. V(D)J enrichment was done using the single cell 5’ VDJ enrichment kit according to the manufacturer’s protocols. Libraries were sequenced on HiSeq4000 (Novogene Inc) with a 70:20:10 mix for gene expression:VDJ:hashing libraries.
scRNAseq; Individual mice are hash-tagged with TotalSeq antibodies. 3-4 mice from each time point were pooled using cell hashes, and run on a GEM. Each timepoint was processed independently through 10x protocol and through Illumina sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
AJ39-VDJ
TCR library
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| Data processing |
Sequence data were downloaded on the Joglekar laboratory server and aligned to the mouse genome (Mm10) using cellranger (10x Genomics Inc). TCR annotation was performed using cellranger vdj using mouse GRCm38 assembly. All three timepoints were sequenced and processed separately. Cellranger and cellranger vdj output files were used as inputs in Seurat
Assembly: Mm10 / GRCm38
Supplementary files format and content: barcodes.tsv, matrix.mtx, and features.tsv files for each run were generated using cellranger count. Filtered.contig.annotations.csv files were generated using cellranger vdj
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| Submission date |
Nov 09, 2023 |
| Last update date |
Feb 19, 2024 |
| Contact name |
Alok Joglekar |
| E-mail(s) |
joglekar@pitt.edu
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| Organization name |
University of Pittsburgh
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| Department |
Immunology
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| Lab |
Joglekar
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| Street address |
Assembly 3045, 5051 Center Ave
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| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15261 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE247410 |
Single cell RNA sequencing on pancreatic islet infiltrating T cells from NOD mice. |
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| Relations |
| BioSample |
SAMN38194656 |
| SRA |
SRX22478471 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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