|
| Status |
Public on Sep 12, 2022 |
| Title |
Patient 5 [LB05] |
| Sample type |
SRA |
| |
|
| Source name |
Metastatic lung cancer in the brain
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Metastatic lung cancer in the brain
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lung FFPE tissues were processed following the GeoMx® DSP slide prep user manual (MAN-10087-04). Before being deparaffinized and hydrated by Leica Biosystems BOND RX, the slides were baked in oven at 60°C for at least 3 hours. And then proteinase K was added to digest the proteins.
Oligoes from PanCK+ and PanCK- regions were collected separately by UV-cleavage. The oligoes then were uniquely indexed using Illumina’s i5 x i7 dual-indexing system. PCR reactions were purified and libraries were paired-end sequenced (2x75) on a NextSeq550.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
LB05
|
| Data processing |
GeoMx® DSP counts from each AOI were scaled to the 75th percentile of expression
Assembly: hg38
Supplementary files format and content: tab-delimited text files include 75th percentile of expression values for each Sample
Library strategy: GeoMx Seq
|
| |
|
| Submission date |
Sep 12, 2022 |
| Last update date |
Feb 26, 2023 |
| Contact name |
Rober Abdo |
| Organization name |
The University of Western Ontario
|
| Department |
Pathology
|
| Lab |
Dental Sciences Building Room 4029
|
| Street address |
1151 Richmond St
|
| City |
London |
| State/province |
ON |
| ZIP/Postal code |
N6A 5C1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE200563 |
Spatial gene expression-based, non-small cell lung carcinoma patients with paired brain metastases |
|
| Relations |
| BioSample |
SAMN30806727 |
| SRA |
SRX17532938 |
