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Sample GSM8120455 Query DataSets for GSM8120455
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

Supplementary file Size Download File type/resource
GSM8120455_DSP-1001660009320-A-B04.dcc.gz 50.5 Kb (ftp)(http) DCC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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