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| Status |
Public on May 04, 2021 |
| Title |
E31 (CS14) (MS135) |
| Sample type |
SRA |
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| Source name |
Cynomolgus monkey embryo E31
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| Organism |
Macaca fascicularis |
| Characteristics |
tissue: embryo
developmental stage: E31
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| Extracted molecule |
total RNA |
| Extraction protocol |
For preparation of E24 (CS11) embryos, the yolk sac and amnion were first carefully trimmed with forceps and ophthalmic scissors, and then the heart (and anterior tissues above the heart) and the posterior growth zone including the PS were removed.
For E28 (CS13) and E31 (CS14) embryos, the heart (and anterior tissues above the heart), and hindlimb (and tissues beneath the hindlimb) were removed, and then the urogenital ridge containing the mesonephros, CE and a portion of the proximal mesentery were isolated. For E37 embryos (CS18), similarly to E28/31 embryos, after the anterior and posterior tissues were removed, the urogenital ridges were isolated en bloc. Subsequently, most mesonephros and mesentery were trimmed, and tissues consisting of predominantly GR with an attached portion of mesonephros, putative adrenal glands and proximal mesentery were used for downstream sample processing.
Isolated embryonic fragments were washed twice with PBS and then minced with scissors in 500 μl of 0.1% trypsin/EDTA solution, then incubated for 9 min at 37°C with gentle pipetting every 3 min. After quenching of the reaction by addition of 500 μl of STO medium, cell suspensions were strained through a 70 µm nylon cell strainer and centrifuged for 220 g for 5 min.
Fragments of cynomolgus monkey embryos at E24 (CS11), E28 (CS13), E31 (CS14) and E37 (CS18) were used for scRNA-seq with a Chromium Single Cell 3ʼ Reagent Kit (v2 chemistry).
Cell pellets were resuspended in 0.1% BSA in PBS, counted, loaded into Chromium microfluidic chips and used to generate single cell gelbead emulsions with a Chromium controller (10x Genomics) according to the manufacturer’s protocol (Chromium Single Cell 3' Reagent Kits v3)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Single cell transcriptome from cynomolgus monkey embryo at E31
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| Data processing |
Raw data were demultiplexed with the mkfastq command in Cell Ranger (v2.1.0) 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 cynomolgus monkeys (MacFas5.0) and obtain the read counts.
Genome_build: MacFas5.0
Supplementary_files_format_and_content: Cell Ranger output, TSV and matrix files
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| Submission date |
Oct 25, 2020 |
| Last update date |
May 05, 2021 |
| 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 |
GPL22523 |
| Series (2) |
| GSE160043 |
The embryonic ontogeny of the gonadal somatic cells in mice and monkeys [10x] |
| GSE160050 |
The embryonic ontogeny of the gonadal somatic cells in mice and monkeys |
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| Relations |
| BioSample |
SAMN16540679 |
| SRA |
SRX9354151 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4855855_E31_barcodes.tsv.gz |
26.3 Kb |
(ftp)(http) |
TSV |
| GSM4855855_E31_genes.tsv.gz |
159.2 Kb |
(ftp)(http) |
TSV |
| GSM4855855_E31_matrix.mtx.gz |
62.6 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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