|
| Status |
Public on Mar 04, 2024 |
| Title |
F140509 Gastric cancer stroma CD68+ ROI 2 |
| Sample type |
SRA |
| |
|
| Source name |
tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: tumor
cell type: CD68 pos
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Probes (photocleaved oligos containing a readout tag sequence identifier and unique molecule identifier) were aspirated by the GeoMx instrument for library preparation.
Following collection on the GeoMx instrument, the probes were subjected to polymerase chain reaction amplification during which i5 and i7 indexing sequences were added. Following subsequent pooling, purification, and qualtity control, the library was sequenced on an Illumina HiSeq4000.
Spatial Transcriptomics
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Spatial transcriptomics by GeoMx Digital Spatial Prolifer
|
| Data processing |
Raw fastq files were converted to DCC files by the Nanostring geomxngspipeline software.
The DCC files were uploaded to the DSP software and the read counts file was exported for furthere analysis.
Assembly: hg38
Supplementary files format and content: DCC files generated by the Nanostring geomxngspipeline software
Supplementary files format and content: Read count files exported from Nanostring GeoMx DSP software
|
| |
|
| Submission date |
Feb 29, 2024 |
| Last update date |
Mar 04, 2024 |
| Contact name |
Lee Benjamin Rivera |
| E-mail(s) |
lrivera@ngmbio.com
|
| Organization name |
NGM Bio
|
| Department |
Biology
|
| Street address |
333 Oyster Point Blvd.
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE260598 |
Anti-tumor activity of a novelLAIR1antagonist in combination with anti-PD-1to treat collagen-rich solid tumors (GeoMx) |
| GSE260599 |
Anti-tumor activity of a novelLAIR1antagonist in combination with anti-PD-1to treat collagen-rich solid tumors |
|
| Relations |
| BioSample |
SAMN40205076 |
| SRA |
SRX23797568 |
