e.g., HRA000087; HRA000150
HRA002336
Title:
Parallel single cell and bulk transcriptome analyses reveal key features of the gastric tumor microenvironment
Release date:
2022-10-01
Description:
We combined bulk and single-cell RNA-sequencing from tumors and matched normal tissue of 24 treatment-naive GC patients to better understand which cell types and transcriptional programs are associated with malignant transformation of the stomach. Clustering 96,623 cell of non-epithelial origin revealed 96 well-defined TME cell types. Activated fibroblasts and endothelial cells were most prominently overrepresented in tumors. Intercellular network reconstruction as well as survival analysis of an independent cohort implied the importance of these cell types together with immunosuppressive myeloid cell subsets and regulatory T cells in establishing an immunosuppressive microenvironment correlating with worsened prognosis and lack of response in anti-PD1 treated patients. In contrast, a subset of IFNg activated T cells and HLA-II expressing macrophages were found to be linked to response and increased overall survival.
Data Accessibility:   
Controlled access Request Data
BioProject:
Study type:
Disease Study
Disease name:
stomach cancer
Data Access Committee

For each controlled access study, there is a corresponding Data Access Committee(DAC) to determine the access permissions. Access to actual data files is not managed by NGDC.


DAC NO.:
DAC name:
DAC_ZhangLab
Contact person:
Cheng Sijin
Email:
chengsj@mail.cbi.pku.edu.cn
Description:
BIOPIC, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences
Individuals & samples
Individual Accession
Individual Name
Gender
Sample Accession
Sample Name
Sample Description
Individual Accession
Individual Name
Gender
Sample Accession
Sample Name
Sample Description
HRI225803D171012maleHRS378542D171012_NAdjacent non-tumor normal Sample from individual D171012
HRI225803D171012maleHRS378543D171012_TTumor Sample from individual D171012
HRI225804D171116femaleHRS378544D171116_NAdjacent non-tumor normal Sample from individual D171116
HRI225804D171116femaleHRS378545D171116_TTumor Sample from individual D171116
HRI225805D171218femaleHRS378546D171218_NAdjacent non-tumor normal Sample from individual D171218
HRI225805D171218femaleHRS378547D171218_TTumor Sample from individual D171218
HRI225806D180116maleHRS378548D180116_NAdjacent non-tumor normal Sample from individual D180116
HRI225806D180116maleHRS378549D180116_TTumor Sample from individual D180116
HRI225807D180118femaleHRS378550D180118_NAdjacent non-tumor normal Sample from individual D180118
HRI225807D180118femaleHRS378551D180118_TTumor Sample from individual D180118
Showing 1 to 10 of 48 rows rows per page
Run accession
Files
Experiment
Experiment title
Platform
Sample
Run accession
Files
Experiment
Experiment title
Platform
Sample
HRR657382HRR657382_f1.fastq.gz (15.60 GB)HRX473082D171012_N_GEXIllumina HiSeq 4000HRS378542 (SAMC2103907)
HRR657382HRR657382_r2.fastq.gz (18.36 GB)HRX473082D171012_N_GEXIllumina HiSeq 4000HRS378542 (SAMC2103907)
HRR657383HRR657383_f1.fastq.gz (15.55 GB)HRX473083D171012_T_GEXIllumina HiSeq 4000HRS378543 (SAMC2103911)
HRR657383HRR657383_r2.fastq.gz (18.57 GB)HRX473083D171012_T_GEXIllumina HiSeq 4000HRS378543 (SAMC2103911)
HRR657384HRR657384_f1.fastq.gz (15.89 GB)HRX473084D171116_N_GEXIllumina HiSeq 4000HRS378544 (SAMC2103915)
HRR657384HRR657384_r2.fastq.gz (18.57 GB)HRX473084D171116_N_GEXIllumina HiSeq 4000HRS378544 (SAMC2103915)
HRR657385HRR657385_f1.fastq.gz (14.81 GB)HRX473085D171116_T_GEXIllumina HiSeq 4000HRS378545 (SAMC2103919)
HRR657385HRR657385_r2.fastq.gz (17.40 GB)HRX473085D171116_T_GEXIllumina HiSeq 4000HRS378545 (SAMC2103919)
HRR657386HRR657386_f1.fastq.gz (13.46 GB)HRX473086D171218_N_GEXIllumina HiSeq 4000HRS378546 (SAMC2103923)
HRR657386HRR657386_r2.fastq.gz (15.91 GB)HRX473086D171218_N_GEXIllumina HiSeq 4000HRS378546 (SAMC2103923)
Showing 1 to 10 of 306 rows rows per page
Submitter:   Zhang Zemin / zemin@pku.edu.cn
Organization:   Peking University
Submission date:   2022-04-25
Requests:   24