|
| Status |
Public on Apr 01, 2024 |
| Title |
KOOTI-WT1 scRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: tumor
cell line: primary cells
cell type: Tumor-infiltrating lymphocyte
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To analyze the function of infiltrating cells in the TME, we sorted tumor-infiltrating lymphocytes from tumor-bearing mice.
Use LUNA-FL™ Automated Fluorescence Cell Counter (logos biosystems) to consult the 10x Genomics Single Cell Protocols Cell Preparation Guide and the Guidelines for Optimal Sample Preparation flowchart (Documents CG00053 and CG000126 respectively) for more information on preparing cells. Libraries were prepared using the Chromium controller according to the 10x chromium Next GEM Single Cell 3’ v3.1 protocol(CG000315). Briefly, the cell suspensions were diluted in nuclease-free water to achieve a targeted cell count of 10,000. Cell suspension was mixed with master mix and loaded with Single Cell 3’V3.1 Gel Beads and Partitioning Oil into a chromium Next GEM chip G. RNA transcripts from single cells were uniquely barcoded and reverse-transcribed within droplets. cDNA molecules were pooled and the cDNA pool then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. The purified libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide(KAPA) and qualified using the Agilent Technologies 4200 TapeStation(Agilent technologies). And then the libraries were sequenced using HiSeq platform(Illumina) according to the read length in the user guide.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
10x chromium Next GEM Single Cell 3’ v3.1 kit
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger v6.1.2 (10x Genomics; https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mouse reference genome (mm10-2020-A)
|
| |
|
| Submission date |
Apr 18, 2023 |
| Last update date |
Apr 01, 2024 |
| Contact name |
YUNA JO |
| E-mail(s) |
yoona8987@gmail.com
|
| Phone |
+821080048987
|
| Organization name |
Pusan National University
|
| Street address |
49, Busandaehak-ro
|
| City |
Yangsan |
| ZIP/Postal code |
50612 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE229993 |
Gene expression profile at the single-cell level of tumor-infiltrating CD8+ T cells from tumor-bearing mice transferred Nrf2-deficient CD8+ T cells or WT CD8+ T cells |
| GSE229994 |
tumor-infiltrating CD8+ T cells from tumor-bearing mice transferred Nrf2-deficient CD8+ T cells. |
|
| Relations |
| BioSample |
SAMN34240141 |
| SRA |
SRX20004787 |
