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| Status |
Public on May 01, 2024 |
| Title |
bladder_Tom_plus |
| Sample type |
SRA |
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| Source name |
bladder
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| Organism |
Mus musculus |
| Characteristics |
tissue: bladder
cell type: All
genotype: p16-CreERT2/R26-LSL-tdTomato
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| Extracted molecule |
total RNA |
| Extraction protocol |
The bladder from a 25-month-old male p16-CreERT2-tdTomato mouse was harvested two weeks after consecutive five days i.p injection of tamoxifen. The harvested bladder tissue was minced using a blade and then subjected to agitation two times using 18 G and 21 G needles during one-hour incubation at 37℃ in 2ml PBS containing 5 mg Collagenase Type 4 (GIBCO) and 5 KU/ml of DNase I (Sigma-Aldrich). The cell suspension was filtered through a 70 µm strainer (Falcon), followed by centrifugation (800 x g, 4℃, 3 minutes). The pellet was then resuspended in a wash buffer (4% FBS in PBS). After pelleting the cells, they were resuspended in wash buffer containing 10% FcR blocking reagent (MACS) for 15 minutes. Subsequently, the cells were stained with an anti-CD45 antibody (Biolegend) for 30 minutes at 4°C in the absence of light. After pelleted, cells were resuspended in wash buffer containing with 0.1 µg/ml DAPI (Cell Signaling Technology) to exclude dead cells during sorting. The CD45-/DAPI-/Tomato+ and CD45-/DAPI-/Tomato- cells were sorted by using BD FACSAria SORP (BD Bioscience).
For the scRNA-seq library construction, we followed the manufacturer’s instructions of 10x Genomics Chromium Single Cell 3′ Reagent Kit v3.1.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
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| Description |
10X Genomics
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| Data processing |
The Cell Ranger package (version 7.0.0) was utilized to process unique molecular identifiers (UMIs) and barcodes and align the transcripts to a mm10 mouse reference genome, which was supplied with tdTomato and WPRE sequences manually.
Assembly: mm10
Supplementary files format and content: tsv files and matrix files
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| Submission date |
Jan 16, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Satoru Meguro |
| E-mail(s) |
smeguro.t.l@gmail.com
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| Phone |
+81245471111
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| Organization name |
Fukushima Medical University
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| Street address |
Hikarigaoka1
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| City |
Fukushima |
| State/province |
Fukushima |
| ZIP/Postal code |
9601295 |
| Country |
Japan |
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| Platform ID |
GPL28457 |
| Series (1) |
| GSE253338 |
Pre-existed senescent fibroblasts in aged bladder create tumor-permissive niche via CXCL12 secretion |
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| Relations |
| BioSample |
SAMN39458718 |
| SRA |
SRX23230660 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8018996_bladder_positive_barcodes.tsv.gz |
14.9 Kb |
(ftp)(http) |
TSV |
| GSM8018996_bladder_positive_features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
| GSM8018996_bladder_positive_matrix.mtx.gz |
24.7 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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