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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 30, 2023 |
| Title |
adult male mouse thymus short-read 10x scRNA-seq, replicate 2 |
| Sample type |
SRA |
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| Source name |
thymus
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| Organism |
Mus musculus |
| Characteristics |
tissue: thymus
cell type: all cells
age: 2 months
Sex: male
colony/strain: C57BL/6J
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| Extracted molecule |
total RNA |
| Extraction protocol |
Thoracic tissue was dissected using sterile surgical techniques and subsequently transferred to a petri dish containing PBS. Fat tissue surrounding the thymic parenchyma was carefully removed with microscissors and tissue forceps under a surgical microscope. Excess liquid/PBS was carefully removed with Kimwipes before weight measurement. For histological analysis, the tissues were fixed in 10% formalin and following standard tissue processing procedures. For the purpose of creating single-cell suspensions, thymic tissues were ground through 100 μm and 40 μm cell strainers (Falcon 352360 and 352340, Corning, NY) with a syringe plunger. Cells were subsequently pelleted (300g, 3 minutes, 4 ̊C), resuspended in 5 mL of ACK lysis buffer (Lonza BP10-548E, Basel, Switzerland) for 5 minutes at room temperature, and washed and resuspended with PBS with 0.04% BSA. Cell density and viability were determined using the Countness II Cell Counter (Thermofisher AMQAF1000). The cells were pelleted and resuspended at 1 million cells per ml of 0.04% BSA/PBS prior generating the 10× GEM single-cell libraries.
Single cells were captured in droplet emulsion using the Chromium Controller (10× Genomics, Pleasanton, CA), and GEM single-cell libraries were constructed according to the 10× Genomics protocol using the Chromium Single-Cell 30 Gel Bead and Library 3’ V3 kit (10× Genomics, Pleasanton, CA). In brief, cell suspensions were diluted in PBS with 0.04% BSA to a final concentration of 1×106 cells/mL (1,000 cells per μL). Cells were loaded in each channel with a target output of 10,000 cells per sample. All reactions were performed in a C1000 Touch Thermal Cycler (Bio-Rad Laboratories, Hercules, CA) with a 96 Deep Well Reaction Module. Twelve cycles were used for cDNA amplification and sample index PCR. Amplified cDNA and final libraries were evaluated using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) with a high sensitivity chip.
paired-end ilimina next-seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
10x Genomics
mouse.male.thymus_2
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| Data processing |
Cell Ranger mkfastq for demultiplexing
Cell Ranger count for generating gene-barcode-matrix
mm10 + Gencode vM25 primary assembly annotation
barcodes.tsv.gz is the gunzipped list of sequenced barcodes. genes.tsv.gz is the gunzipped list of sequenced genes. matrix.mtx.gz is the gunzipped compressed sparse gene-barcode-matrix
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| Submission date |
Sep 28, 2022 |
| Last update date |
Nov 30, 2023 |
| Contact name |
Nimrod Daniel Rubinstein |
| E-mail(s) |
[email protected]
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| Phone |
9193082834
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| Organization name |
Calico
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| Street address |
1170 Veterans blvd
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| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE214390 |
The evolution of the naked mole-rat T cells |
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| Relations |
| BioSample |
SAMN31066296 |
| SRA |
SRX17738222 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6605134_mouse.male.thymus_2_barcodes.tsv.gz |
18.5 Mb |
(ftp)(http) |
TSV |
| GSM6605134_mouse.male.thymus_2_genes.tsv.gz |
455.9 Kb |
(ftp)(http) |
TSV |
| GSM6605134_mouse.male.thymus_2_matrix.mtx.gz |
42.1 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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