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| Status |
Public on May 25, 2021 |
| Title |
The ovotestes of zig-zag eel |
| Sample type |
SRA |
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| Source name |
ovotestes
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| Organism |
Mastacembelus armatus |
| Characteristics |
tissue: ovotestes
age: 2-year-old
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| Extracted molecule |
total RNA |
| Extraction protocol |
The dissected ovotestes were cut into pieces in phosphate-buffered saline solution and digested with 0.25% trypsin (Invitrogen, Carlsbad, CA, USA) in Hanks balanced salt solution (Invitrogen) for 30 min at 37 °C. After that, DMEM containing 10% serum was used to terminate digestion. The tissue and cells were gently triturated, centrifuged at 200 g for 5 min, and resuspended with PBS. Cells were filtered with a 0.45-μm cell-strainer to discard any undigested tissue.
Single-cell RNA seq (scRNA-seq) libraries were constructed using a 10X Genomics kit (ChromiumTM Single Cell 3’v2) following the manufacturer’s instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Data processing |
Cell Ranger mkfastq pipeline was performed to demultiplex BCL files and to convert barcode and read data to FASTQ files for analysis Cell Ranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, and UMI counting
Genome_build: NCBI Accession No. PRJNA489256
Supplementary_files_format_and_content: matrix.mtx.gz (tab-delimited text file, the rows of which report the genes in the order they are presented along rows in matrix.mtx.gz)
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| Submission date |
May 24, 2021 |
| Last update date |
May 25, 2021 |
| Contact name |
Zhen Huang |
| E-mail(s) |
zhuang@fjnu.edu.cn
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| Phone |
15960038226
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| Organization name |
Fujian Normal University
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| Street address |
1 keji road, college of life science, Fujian Normal University (Qishan campus)
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| City |
Fuzhou |
| State/province |
Fujian |
| ZIP/Postal code |
350117 |
| Country |
China |
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| Platform ID |
GPL30187 |
| Series (1) |
| GSE175406 |
Bulk and single-cell RNA-seq reveal the role of dmrtb1 in a sequentially hermaphroditic fish, Mastacembelus armatus |
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| Relations |
| BioSample |
SAMN19316667 |
| SRA |
SRX10971144 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5333024_barcodes.tsv.gz |
14.4 Kb |
(ftp)(http) |
TSV |
| GSM5333024_features.tsv.gz |
137.6 Kb |
(ftp)(http) |
TSV |
| GSM5333024_matrix.mtx.gz |
8.9 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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