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| Status |
Public on Aug 01, 2022 |
| Title |
8wpf_#1 |
| Sample type |
SRA |
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| Source name |
fetal ovary
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| Organism |
Macaca fascicularis |
| Characteristics |
developmental stage: fetal
age: 8 wpf
tissue: ovary in vivo
in vitro culture period: -
scrna-seq protocol: Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3 (Single Index)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Fetal ovaries collected from monkey fetuses at 8-18 wpf were carefully dissected out in chilled PBS. Fetal ovaries at 8-14 wpf were minced with scissors in 0.05% trypsin/EDTA/PBS solution (GIBCO, 15400-054), then incubated for 15 min at 37℃ with gentle pipetting every 5 min. Dissociation medium [DMEM (GIBCO, 10313021) containing 10% FBS, 2mM L-glutamine (GIBCO, 25030081), 1X penicillin/streptomycin (GIBCO, 15070063), and 100μg/mL DNaseI (MERCK, DN25)] was added for further dissociation. For fetal ovaries at 16 and 18 wpf, minced tissues were incubated in Accumax (Innovative Cell Technologies, AM105) for 40 min at 37℃ with gentle pipetting every 5 min. Dissociation medium was added for further dissociation. Cell suspensions were further treated with TryPLE Express (1X) (GIBCO, 12604021) for 5min at 37℃ to make the single-cell suspension. Dissociated cells from monkey fetal ovaries and cultured monkey rOvaries were stained with DRAQ7 to distinguish dead cells. All DRAQ7(-) live cells were collected by using FACS (BD Biosciences, FACS Aria III).
The cDNA library for NGS was conducted with Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (Single Index) or Next GEM single cell 3' Library & Gel beads kit ver 3.1 (Single Index) according to the manufacturer’s instructions.
scRNA-seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Single cell transcriptome of monkey fetal ovary in vivo
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| Data processing |
Raw data were demultiplexed with the mkfastq command in Cell Ranger (v5.0.1) with default setting to generate fastq files. The fastq files were processed with count command in Cell Ranger with default setting to map to the reference genome for Macaca fascicularis genome, macFas5.0.
Cell Ranger count command were also performed with "--include-intron" option (data with "_include_intron" marked) and with transcript reference including long non-coding RNAs (data marked with "_include_lncRNA").
Genome_build: macFas5.0
Supplementary_files_format_and_content: Cell Ranger output
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| Submission date |
Jan 24, 2022 |
| Last update date |
Aug 01, 2022 |
| Contact name |
Yukihiro Yabuta |
| E-mail(s) |
yabyab@anat2.med.kyoto-u.ac.jp
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| Organization name |
Kyoto University, Graduate school of medicine
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| Department |
Anatomy and Cell Biology
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| Street address |
Yoshida-Konoe-cho, Sakyo-ku
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| City |
Kyoto |
| State/province |
Kyoto |
| ZIP/Postal code |
606-8501 |
| Country |
Japan |
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| Platform ID |
GPL28212 |
| Series (2) |
| GSE194264 |
Ex vivo reconstitution of fetal oocyte development in humans and cynomolgus monkeys [10x_macfas] |
| GSE194266 |
Ex vivo reconstitution of fetal oocyte development in humans and cynomolgus monkeys |
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| Relations |
| BioSample |
SAMN25226546 |
| SRA |
SRX13883210 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5831846_8wpf_1_filtered_barcodes.tsv.gz |
32.8 Kb |
(ftp)(http) |
TSV |
| GSM5831846_8wpf_1_filtered_features.tsv.gz |
173.3 Kb |
(ftp)(http) |
TSV |
| GSM5831846_8wpf_1_filtered_matrix.mtx.gz |
89.4 Mb |
(ftp)(http) |
MTX |
| GSM5831846_8wpf_1_include_intron_filtered_barcodes.tsv.gz |
37.0 Kb |
(ftp)(http) |
TSV |
| GSM5831846_8wpf_1_include_intron_filtered_features.tsv.gz |
173.3 Kb |
(ftp)(http) |
TSV |
| GSM5831846_8wpf_1_include_intron_filtered_matrix.mtx.gz |
121.9 Mb |
(ftp)(http) |
MTX |
| GSM5831846_8wpf_1_include_lncRNA_filtered_barcodes.tsv.gz |
32.8 Kb |
(ftp)(http) |
TSV |
| GSM5831846_8wpf_1_include_lncRNA_filtered_features.tsv.gz |
190.1 Kb |
(ftp)(http) |
TSV |
| GSM5831846_8wpf_1_include_lncRNA_filtered_matrix.mtx.gz |
92.5 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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