 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 19, 2022 |
| Title |
CC23_responder |
| Sample type |
SRA |
| |
|
| Source name |
TIL infusion product
|
| Organism |
Homo sapiens |
| Characteristics |
individual: patient id CC23
disease state: cervical cancer
Stage: III to IV
treatment: TIL plus CCRT
response: responder
|
| Treatment protocol |
Patients were treated with external-beam radiotherapy (EBRT) to a dose 45Gy for the primary tumor and regional lymphatics at risk. The primary cervical tumor was then boosted, using brachytherapy, with an additional 30 to 40Gy for a total point a dose of ≥ 85Gy. During EBRT, cisplatin was given weekly 30 to 40 mg/m2 for a maximum of 6 doses. Ex vivo expanded auto-TIL was infused 1 day after the completion of CCRT and brachytherapy. After cell infusion, Interleukin-2 (IL-2) was administered as an IM bolus at 400,000 IU/dose every 24 hours to 7 doses
|
| Growth protocol |
In brief, the fresh tumor samples were collected in Roswell Park Memorial Institute (RPMI) 1640 medium with antibiotics and resected into small fragments, and enzymatic dissociated into single-cell suspension by collagenase type IV (0.1 mg/mL, Sigma-Aldrich), and then planted into 24-well cell culture plates in X-vivo (Lonza) culture medium containing recombinant human interleukin-2 (IL-2, 1000 IU/mL) for 1 to 2 weeks to get the purified T cells. Once a sufficient number of T cells (>10 *10^6) was generated, they were cryopreserved for further expansion. Clinical infusion products were generated by a rapid expansion protocol (REP) for “young TILs”: Cryopreserved TILs were thawed and further expanded to treatment levels using an anti-CD3 antibody (OKT-3, 30 ng/mL, R&D Systems) and 3500IU/ml IL-2 (Beijing sihuan pharmaceutical company) and irradiated feeder cells for 14 days under conditions in accordance with current good manufacturing practices (GMP) in the Biotherapy Center at Sun Yat-sen University Cancer Center.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All steps from single-cell encapsulation to library preparation were done at BGI-Shenzhen, completing as per manufacturer’s instructions. Single cell capture, cDNA synthesis and preamplification was constructed using DNBelab C4-V1 system. And libraries were sequenced at the MGISEQ2000 platforms.
RNA libraries were prepared for sequencing using standard MGISEQ2000 protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MGISEQ-2000RS |
| |
|
| Description |
instrument model: DNBSEQ-T1&T5
|
| Data processing |
Raw single-cell RNA-seq data were processed using the program PISA (https://github.com/shiquan/PISA), including the gene expression data was mapped to human genome reference sequence (GRCh38). A number of steps were performed to filter out poor quality data. Firstly, cells for which with < 200 expressed genes or > 15% of detected genes linked to mitochondrial genes were removed. Secondly, Genes detected in fewer than three cells and cells with more than 7,000 detected genes were filtered out. Thirdly, The R package DoubletFinder was applied to remove doublets, with an expected doublet rate of 0.04.
For downstream analyses, the R package Seurat (4.0.0) was applied to normalize the raw count matrix to identify highly variable genes, scale genes, and integrate samples. Next, we clustered and visualized the cells using a graph-based clustering approach.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files containing gene/barcode matrices for each Sample
|
| |
|
| Submission date |
Dec 02, 2021 |
| Last update date |
Jul 19, 2022 |
| Contact name |
jiang li |
| E-mail(s) |
lijiang@sysucc.org.cn
|
| Organization name |
Sun yat-sen university
|
| Street address |
651 Dongfeng East Road, Yuexiu District, Guangzhou
|
| City |
Guangzhou |
| ZIP/Postal code |
510030 |
| Country |
China |
| |
|
| Platform ID |
GPL30209 |
| Series (1) |
| GSE190075 |
Adoptively transferred tumor-infiltrating lymphocyte immunotherapy following concurrent chemoradiotherapy in patients with advanced cervical cancer: a phase 1 trial |
|
| Relations |
| BioSample |
SAMN23574399 |
| SRA |
SRX13294011 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5712856_CC23_barcodes.tsv.gz |
9.9 Kb |
(ftp)(http) |
TSV |
| GSM5712856_CC23_features.tsv.gz |
85.8 Kb |
(ftp)(http) |
TSV |
| GSM5712856_CC23_matrix.mtx.gz |
19.4 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
