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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 04, 2020 |
| Title |
LZ018 (iNOA_2) |
| Sample type |
SRA |
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| Source name |
testis tissue
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| Organism |
Homo sapiens |
| Characteristics |
disease state: Non -obstructive azoospermia (NOA)
tissue: testis
condition: pathologic
group: iNOA_2
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit (P/N 120237, 10× Genomics) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina Novaseq 6000)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Cell Ranger software (version 2.2.0), provided by 10× Genomics, was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and downsample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
Cells were further filtered according to the following threshold parameters: the total number of expressed genes, 500 to 9000; total UMI count, less than 35,000; and proportion of mitochondrial genes expressed, <40%.
Genome_build: hg18
Supplementary_files_format_and_content: UMI values for each cell
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| Submission date |
Apr 28, 2020 |
| Last update date |
Sep 05, 2020 |
| Contact name |
Liangyu Zhao |
| E-mail(s) |
zhaoly37@mail.sysu.edu.cn
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| Phone |
+86 18801902577
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| Organization name |
Shanghai Jiao Tong University School of Medicinethe Fifth Affiliated Hospital of Sun Yat-sen University
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| Street address |
52th Meihua Road, Zhuhai, China
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| City |
Zhuhai |
| State/province |
Guangdong |
| ZIP/Postal code |
519000 |
| Country |
China |
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| Platform ID |
GPL27644 |
| Series (1) |
| GSE149512 |
Single-cell analysis of developing and azoospermia human testicles reveals central role of Sertoli cells |
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| Relations |
| BioSample |
SAMN14445369 |
| SRA |
SRX8082039 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4504196_LZ018matrix.csv.gz |
14.2 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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