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| Status |
Public on Apr 15, 2024 |
| Title |
Ovary,young-1,spatial |
| Sample type |
SRA |
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| Source name |
ovary
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| Organism |
Homo sapiens |
| Characteristics |
tissue: ovary
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Human ovary tissues were saved in tissue storage solution (Miltenyi, 130-100-008) at ice bath and transferred to laboratory within two hours. Then we get rid of damaged parts in light microscopy and cut out a ~1 cm3 piece for isolation. The tissue was washed with PBS (containing 0.04% BSA) and cut into 0.1 cm3 in 2 mg/ml IV collagenase. Then the tube containing IV collagenase and tissues was oscillated in water bath at 37℃ for 20 min. After centrifuged for 5 min on 1200 rpm the supernatant was discarded and resuspended in 0.5% trypsin. Then the tissues in 0.5% trypsin were oscillated in water bath at 37℃ for 10 min again. Digestion was stopped with DMEM containing 10% BSA and filtered with 40 μm cell strainer (Millipore). Finally, cells were incubated in red blood bell lysis buffer for 10 min then centrifuged and resuspended in 100-200 μL PBS containing 0.04% BSA. For spatial transcriptome sequencing, ovary tissues were cut into about 10*10*5 mm piece and dried with lab blotting paper to prevent ice crystal formation. After that we embedded the tissue with opti-mum cutting temperature compound into the embedding box in dry ice and saved in -80 ℃.
Single-cell suspension for each ovary sample was loaded onto a separate channel of a Chromium 10x Genomics single cell 3’v3 library chip as per manufacturer’s protocol. cDNA sequencing libraries were prepared according to the manufacturer’s protocol and sequenced on an Illumina Novaseq 6000 (2x150bp paired-end reads). Spatial transcrintome seauencing libraries were prepared with 10xGenomics Visium Soatail Gene Exoression Slides & Reagent kit according to manufacturer's construction
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Fresh frozen Spatial transcriptome sequencing
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| Data processing |
Raw sequence reads in FASTQ format from ovary samples were processed and aligned to the GRCh38 human reference transcriptome (https://www.10xgenomics.com/) using the Cellranger v4.0.0 pipeline (https://www.10xgenomics.com/) with default parameters.
Assembly: GRCh38
Supplementary files format and content: matrix files
Library strategy: spatial transcriptomic
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| Submission date |
Feb 13, 2024 |
| Last update date |
Apr 15, 2024 |
| Contact name |
Shixuan Wang |
| E-mail(s) |
shixuanwang@tjh.tjmu.edu.cn
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| Organization name |
Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology
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| Street address |
Jiefang Avenue
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430030 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE255690 |
Spatiotemporal transcriptomic changes of human ovarian aging and the key regulatory role of FOXP1 |
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| Relations |
| BioSample |
SAMN39910477 |
| SRA |
SRX23593524 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8077825_st_young-1_barcodes.tsv.gz |
17.3 Kb |
(ftp)(http) |
TSV |
| GSM8077825_st_young-1_features.tsv.gz |
287.6 Kb |
(ftp)(http) |
TSV |
| GSM8077825_st_young-1_matrix.mtx.gz |
12.3 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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