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| Status |
Public on Feb 24, 2023 |
| Title |
Ovary, anestrus |
| Sample type |
SRA |
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| Source name |
Ovary
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| Organism |
Bos grunniens |
| Characteristics |
tissue: Ovary
age: 4 years old
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| Extracted molecule |
total RNA |
| Extraction protocol |
The pieces of ovarian tissue were washed in cooled RPMI 1640 medium containing 0.04% bovine serum albumin twice. The ovarian samples were further minced into approximate 0.5 mm3 pieces with a sterile scalpel blade in RPMI 1640 medium containing 0.04% BSA. The pieces were incubated with 1 mg/ml collagenase Type II in 0.25% trypsin-EDTA on ice overnight. The digestion was stopped by adding 10% of fetal calf serum. Next, the dissociated cells were collected by centrifugation at 160 × g for 3 min and incubated with advanced DMEM/F12 Glutamax containing 1% insulin-transferrin-selenium , 1% penicillin-streptomycin, and 27 IU/ml RNase-free DNase I at 37 °C for 1 h. The ovarian cells were resuspended in DPBS containing 2% FBS and passed through a 40 μm cell strainer.
The cell suspensions containing high viability cells were prepared immediately. Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (Chromium, PN-1000128) was used for gel beads in emulsion (GEM) formation. The cell suspensions, gel beads, and partitioning oil were loaded into a Chromium Single Cell Controller to produce single-cell GEM. Then, a primer containing Illumina TruSeq Read 1, 10X Barcode, and unique molecular identifier (UMI) was applied to produce barcoded full-length cDNA by reverse transcriptase reaction. The GEMs were broken and the pooled fractions were recovered. The first-strand cDNAs were purified with silane magnetic beads and amplified to generate sufficient mass for library construction. Enzymatic fragmention and size selection were used to optimize cDNA amplicon size. P5, P7, a sample index, and a TruSeq Read 2 were added to the amplicon via end repair, A-tailing, adaptor ligation, and PCR.
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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 |
10x Genomics
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| Data processing |
Raw scRNA-seq data was converted using the Cell Ranger analysis pipeline provided by 10X Genomics (v2.2.0) and reads were aligned to the yak genome version BosGru3.0 using the STAR aligner.
Assembly: BosGru3.0
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Sep 22, 2022 |
| Last update date |
Feb 24, 2023 |
| Contact name |
Jie Pei |
| E-mail(s) |
peijie@caas.cn
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| Organization name |
Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences
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| Street address |
No. 335 Jiangouyan ST, Qilihe District
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| City |
Lanzhou |
| State/province |
Gansu |
| ZIP/Postal code |
730050 |
| Country |
China |
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| Platform ID |
GPL30409 |
| Series (1) |
| GSE213989 |
Dynamic changes in cellular atlases and communication patterns within yak ovaries across diverse reproductive states unveiled by single-cell analysis [scRNAseq_Yak_Ovary_Anestrus_2] |
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| Relations |
| BioSample |
SAMN30965614 |
| SRA |
SRX17677118 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6597589_Apr_2_barcodes.tsv.gz |
20.0 Mb |
(ftp)(http) |
TSV |
| GSM6597589_Apr_2_features.tsv.gz |
214.1 Kb |
(ftp)(http) |
TSV |
| GSM6597589_Apr_2_matrix.mtx.gz |
94.7 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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