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| Status |
Public on Dec 07, 2023 |
| Title |
Trigeminal ganglion (TG) cells, replicate 1, scRNAseq |
| Sample type |
SRA |
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| Source name |
trigeminal ganglion non-neuronal cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: Non-neuronal
tissue: trigeminal ganglia
strain: C57BL/6
age: 6-8 weeks old
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| Extracted molecule |
total RNA |
| Extraction protocol |
Freshly collected trigeminal ganglia from wild-type untreated male C57black/B6 mice were treated by Librase (200ug/ml) and dispase II (300ug/ml) in Hanks for 60 min at 37 degree. Single cell susupension was generated by prituration of digested trigeminal ganglia. Suspension was filtered through 70um filter. Live cells were FACS sorted. Trigeminal ganglion cells were resuspended in DPBS supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 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 |
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 v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Aug 09, 2023 |
| Last update date |
Dec 07, 2023 |
| Contact name |
YI ZOU |
| E-mail(s) |
zou@uthscsa.edu
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| Organization name |
UTHSA-GCCRI
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| Street address |
8403 Floyd Curl Drive
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| City |
SAN ANTONIO |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE240432 |
Gene expression profile at single cell level of trigeminal ganglion non-neuronal cells |
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| Relations |
| BioSample |
SAMN36904917 |
| SRA |
SRX21310259 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7697897_Non-neuronalCells_TG_barcodes.tsv.gz |
13.2 Kb |
(ftp)(http) |
TSV |
| GSM7697897_Non-neuronalCells_TG_features.tsv.gz |
244.7 Kb |
(ftp)(http) |
TSV |
| GSM7697897_Non-neuronalCells_TG_matrix.mtx.gz |
12.9 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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