|
| Status |
Public on Apr 09, 2024 |
| Title |
Patient CAN043 ROI 006 |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung
patient id: CAN043
disease: ES-SCLC
age: 78
Sex: Male
smoking status: Former smoker
ecog performance status at baseline: 1
cns metastases at baseline: No
liver metastases at baseline: Yes
bone metastases at baseline: No
platinum administered: Carboplatin
best recist response to treatment: Stable disease
date of first dose of treatment: 05/04/2021
date of last dose of treatment: 10/26/2021
disease progression or death of disease: Yes
disease progression or death: Yes
death: Yes
death of disease: Yes
date of disease progression or death: 10/18/2021
date of death: 11/27/2021
date of last follow-up: 11/27/2021
treatment: durvalumab + carboplatin/cisplatin + etoposide
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Formalin-fixed tissue were paraffin embedded (FFPE), 5-mm tissue sections were cut with microtome.
Spatial transcriptome sequencing libraries were prepared according to GeoMx Digital Spatial Profiler (DSP) NGS Readout User manual (MAN-10153-04).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
CAN-042 CAN-043 | 006 | Full ROI
|
| Data processing |
Raw sequencing data FASTQ files were generated using Illumina NextSeq 2000 instrument.
Raw sequencing data FASTQ files were processed using GeoMx NGS Pipeline software version 3.1 to generate DCC files.
DCC files were uploaded on to the GeoMx DSP instrument to obtain gene expression raw count data.
Quality control (QC) and Q3 normalization of mRNA data were performed using the GeoMx Digital Spatial Profiler (DSP) software.
Assembly: GRCh38.p13
Supplementary files format and content: .dcc and .pkc files.
Supplementary files format and content: CANTABRICO_DSP_rawcounts.xlsx: gene expression raw count data.
Supplementary files format and content: CANTABRICO_DSP_normalizedcounts.xlsx: gene expression normalized count data.
Supplementary files format and content: .png: image of tissue and ROIs.
Library strategy: spatial transcriptomics
|
| |
|
| Submission date |
Mar 11, 2024 |
| Last update date |
Apr 09, 2024 |
| Contact name |
Jon Zugazagoitia |
| E-mail(s) |
[email protected]
|
| Organization name |
Hospital Universitario 12 de Octubre
|
| Department |
Medical Oncology
|
| Lab |
Tumor Microenvironment and Immunotherapy
|
| Street address |
Avenida de Cordoba s/n
|
| City |
Madrid |
| ZIP/Postal code |
28041 |
| Country |
Spain |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE261345 |
Spatially preserved multi-region transcriptomic subtyping and biomarkers of outcome with chemoimmunotherapy in extensive-stage small cell lung cancer [CANTABRICO_DSP cohort] |
|
| Relations |
| BioSample |
SAMN40379449 |
| SRA |
SRX23902027 |
