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| Status |
Public on May 03, 2024 |
| Title |
CD, replicated 1, scRNA-seq |
| Sample type |
SRA |
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| Source name |
testis
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| Organism |
Mus musculus |
| Characteristics |
tissue: testis
strain: ICR
Sex: male
treatment: conventional diet (CD)
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| Extracted molecule |
total RNA |
| Extraction protocol |
The fresh tissues were stored in the sCelLiveTM Tissue Preservation Solution (Singleron) on ice after the surgery within 30 mins. The specimens were washed with Hanks Balanced Salt Solution (HBSS) for three times, minced into small pieces, and then digested with 3 mL sCelLiveTM Tissue Dissociation Solution (Singleron) by Singleron PythoN™ Tissue Dissociation System at 37 °C for 15 min. The cell suspension was collected and filtered through a 40-micron sterile strainer. Afterwards, the GEXSCOPE® red blood cell lysis buffer (RCLB, Singleron) was added, and the mixture[Cell: RCLB=1:2 (volume ratio)] was incubated at room temperature for 5-8 min to remove red blood cells. The mixture was then centrifuged at 300 × g 4 ℃ for 5 mins to remove supernatant and suspended softly with PBS
Single-cell suspensions (2×105 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) (Ref). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Sample 1_CD
10x Genomics
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| Data processing |
Raw reads from scRNA-seq were processed to generate gene expression matrixes using an internal pipeline.
Raw reads were processed to generate gene expression Matrix using SCOPE-tools
Barcodes and UMIs were extracted from R1 reads and corrected. Adapter sequences and poly A tails were trimmed from R2 reads and the trimmed R2 reads were employed STAR for the alignment of reads against the GRCm38 mouse reference genome.
The reads were localized to the genome, further localized to the genes by utilizing the featureCounts software.
The functions from Seurat was used for dimension-reduction and clustering. Then we used NormalizeData and ScaleData funcitons to normalize and scale all gene expression, and selected the top 2000 variable genes with FindVariableFeautres function for PCA analysis. !Sample_data_processing = Using the top 20 principle components, we separated cells into multiple clusters with FindClusters.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files
the '*update.tar.gz' contains the files processed with CeleScope v1.15.0, while the '.tsv' and '.mtx' files with CeleScope v1.4.0.
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| Submission date |
Jul 27, 2023 |
| Last update date |
May 03, 2024 |
| Contact name |
Wenbin Cao |
| E-mail(s) |
caowenbin@stu.xjtu.edu.cn
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| Organization name |
Xi'an Jiaotong University
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| Street address |
76 Yanta West Road, Xi’an, Shaanxi 710061, China
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| City |
Xi'an |
| State/province |
Shanxi |
| ZIP/Postal code |
710061 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE239391 |
Single-cell RNA sequencing Reveals Obesity-Induced Inhibition of Testosterone Production and Damage of Blood-Testis Barrier Integrity |
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| Relations |
| BioSample |
SAMN36727265 |
| SRA |
SRX21172749 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7664011_Sample_1_CD_barcodes.tsv.gz |
53.2 Kb |
(ftp)(http) |
TSV |
| GSM7664011_Sample_1_CD_genes.tsv.gz |
219.1 Kb |
(ftp)(http) |
TSV |
| GSM7664011_Sample_1_CD_matrix.mtx.gz |
82.8 Mb |
(ftp)(http) |
MTX |
| GSM7664011_Sample_1_CD_matrix_update.tar.gz |
107.0 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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