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| Status |
Public on Mar 13, 2024 |
| Title |
ovCHA039, scTCR-seq |
| Sample type |
SRA |
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| Source name |
Fallopian tube
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| Organism |
Homo sapiens |
| Characteristics |
patient: ovCHA039
tissue: Fallopian tube
cancer stage: 1
metastatic/primary: Primary
chemotherapy: N
recurrent/primary: Primary
platform: Single Cell TCR
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor tissues were minced and dissociated using the enzyme mix from Tumor Dissociation Kit, human (130-095-929, Miltenyi Biotec) with the h_tumor_02 program twice on the gentleMACS dissociator/C tube (130-093-237, Miltenyi Biotec). At the end of each program, the sample was incubated in a pre-warmed 37°C incubator for 30 minutes. The reaction was stopped with a medium containing penicillin-streptomycin and FBS. Then, the sample was filtered through a 70-μm strainer filter (352350, Life Technologies) and processed with Ficoll-Paque PLUS (17-1440-02, GE Healthcare) to remove dead cells. Cell pellets were washed and resuspended in a cell-freezing medium and stored in liquid nitrogen.
Single cell suspensions were subjected to 5' single-cell RNA sequencing using the Single Cell 5′ Library and Gel Bead Kit V1, Single Cell A Chip Kit, i7 Multiplex Kit (10x Genomics) according to the manufacturer's protocol. Library for T92 was constructed using the Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1, and Chromium Next GEM Chip G Single Cell Kit (10x Genomics) instead. Each target for cell recovery was set at 5,000-7,000 cells. TCR-enriched and BCR-enriched libraries were prepared using the Single Cell V(D)J Enrichment Kit, Human T Cell, and Single Cell V(D)J Enrichment Kit, Human B Cell (10× Genomics) according to the manufacturer's protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
ovCHA039_TCR_filtered_contig_annotations.csv
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| Data processing |
Sequencing reads were mapped to the GRCh38 human reference genome using the Cell Ranger toolkit (version 5.0.0).
Assembly: GRCh38
Supplementary files format and content: R object file
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| Submission date |
Aug 18, 2023 |
| Last update date |
Mar 13, 2024 |
| Contact name |
hiram kang |
| E-mail(s) |
khr1138@gmail.com
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| Organization name |
Catholic university of Korea
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| Street address |
222, Banpo-daero, Seocho-gu, Seoul
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| City |
seoul |
| State/province |
seoul |
| ZIP/Postal code |
06591 |
| Country |
South Korea |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE241221 |
Altered tumor signature and T-cell profile after chemotherapy reveal new therapeutic opportunities in High-Grade Serous Ovarian Carcinoma |
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| Relations |
| BioSample |
SAMN37051133 |
| SRA |
SRX21415706 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7719631_ovCHA039_TCR_filtered_contig_annotations.csv.gz |
2.5 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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