NGDC - GSA for Human

HRA005361

HRA005361.xlsx

Title:

T-bet+ CD8+ T cells govern anti-PD-1 responses in microsatellite-stable gastric cancers

Release date:

2023-08-23

Description:

FFPE samples of ICI-12 (partial response, MSI-H) and GC-97(potential responder, MSS) were firstly stained with mIHC protocol described above to identify the locations of T-bet+-PD-L1+ niches. Then adjacent FFPE slides were processed following the GeoMx DSP slide preparation user manual. Slides were baked in an oven at 60 °C for at least 3 h to retrieve antigens. Proteinase K was added to digest the proteins after deparaffination and hydration. The slides were incubated with WTA probe mix overnight. On the second day, the slides were stained with PD-L1, CD45, PanCK, and Syto13 for 2 h. Three concentric circles on each T-bet+-PD-L1+ niche were chosen as regions of interest (ROIs). Oligoes from ROIs were collected by UV-cleavage. PCR reactions were purified. Libraries were paired-end sequenced. Raw counts of all ROIs were obtained by GeoMx DSP data analysis software. Reads were further normalized using Q3 normalization approach with background subtraction.

Data Accessibility:

Controlled access Request Data

BioProject:

PRJCA019016

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.:

HDAC002964

DAC name:

Yunpeng Liu

Contact person:

Liu Yunpeng

Email:

ypliu@cmu.edu.cn

Description:

Professor Yunpeng Liu, Department of Medical Oncology, the First Hospital of China Medical University.

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