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| Status |
Public on May 18, 2024 |
| Title |
Ovary cortex-medulla, vitrified, slice 1 & 2 |
| 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 |
total RNA |
| Extraction protocol |
Human ovarian tissues were donated from one patient aged 35 years who underwent oophorectomy due to cervical cancer. The ovarian tissues were removed using scissors rather than electrocoagulation. Obtained ovarian tissues were directly placed in sterile transport medium (Leibovitz抯 L-15 Medium supplemented with 1% HSA) and transported on ice to the laboratory. In the laboratory, the ovarian tissues were transferred to 10 cm sterile dishes containing chilled sterile normal saline. The saline was changed several times during the process. After most of the medulla was removed with scalpels, the tissues were cut into 10?? mm pieces and divided into fresh and two cryopreservation groups. According to the Stereo-Seq protocol, one piece of fresh group tissues was fixed in O.C.T. compound (Tissue Tek) for subsequent sequencing, tissues of the two cryopreservation groups were processed after freezing and thawing. The tissue capture area was approximately 10? mm. 10?m tissue sections were cut using cryo-microtome (CM1950, Leica) with head temperature set at -16 癈 and adhered to the Stereo-seq chip (BGI) surface. The sections were then performed histomorphology detection, staining in hematoxylin for 3 min, 10 s in bluing agent, and 1 min in eosin. To release mRNA from the cells, the sections were permeabilized, the optimal time was 22 min. After in situ reverse transcription, the resulting cDNAs were amplified.
PCR products were purified for DNA nanoball (DNB) generation and finally sequenced on MGI DNBSEQ-Tx sequencer; detailed protocols are available on the BGI Stereo-seq website (https://en.stomics.tech/).
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
DNBSEQ-T7 |
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| Data processing |
We used STOmics Analysis Workflow (SAW), the official data processing pipeline to perform read quality control, genome mapping and gene expression quantification. Prior to genome mapping, we employed the ST_BarcodeMap module for filtering and mapping of chip identifiers (CID) from sequenced reads to their corresponding chip locations, and FastP for quality control and trimming of the reads. The reads were then mapped to the GRCh38 reference genome with STAR and counted for each spot with Bam2Gem.
Assembly: GRCh38
Supplementary files format and content: bin50.rds - bin50 spots of all samples with preprocessed meta data after preprocessing
Supplementary files format and content: fresh.tissue.gem.gz - SAW pipeline output gem file (fresh)
Supplementary files format and content: slow.tissue.gem.gz - SAW pipeline output gem file (slow)
Supplementary files format and content: vitri.tissue.gem.gz - SAW pipeline output gem file (vitri)
Library strategy: Stereo-seq
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| Submission date |
May 13, 2024 |
| Last update date |
Jan 23, 2025 |
| Contact name |
Kun MA |
| E-mail(s) |
chrissymkcn@gmail.com
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| Phone |
56493222
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| Organization name |
The University of Hong Kong
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| Street address |
No 12 Kam Ling Court Whitty Street Sai Wan HK Island
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| City |
HK |
| State/province |
Hong Kong |
| ZIP/Postal code |
000000 |
| Country |
Hong Kong |
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| Platform ID |
GPL29480 |
| Series (1) |
| GSE267323 |
High-Resolution Spatial Transcriptomics Reveals Stroma Damage in Human Ovarian Tissue Response to Cryopreservation |
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| Relations |
| BioSample |
SAMN41382729 |
| SRA |
SRX24536108 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8263908_B01320B6.gem.gz |
323.9 Mb |
(ftp)(http) |
GEM |
| GSM8263908_vitri.barcodeToPos.h5 |
4.2 Gb |
(ftp)(http) |
H5 |
| GSM8263908_vitri_image.tar.gz |
1.1 Gb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
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