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Sample GSM7657719 Query DataSets for GSM7657719
Status Public on May 21, 2024
Title WM4237-1, mouse 1337, untreated, sample S3
Sample type SRA
Source name WM4237-1 melanoma PDX
Organism Mus musculus
Characteristics tissue: WM4237-1 melanoma PDX
model: WM4237-1
treatment: none
Treatment protocol No treatment
Growth protocol Subcutaneously implanted solid tumor on NSG mouse, passage 0
Extracted molecule total RNA
Extraction protocol OCT-embedded fresh frozen tissue was used. Five 10µm sections from each block were used for total RNA extraction (Qiagen), which was used for RNA integrity determination by RINe score using an Agilent Tapestation and High Sensitivity RNA ScreenTape. Blocks with RINe greater than 7 were optimized for ideal permeabilization time following the vendor protocol (10x Genomics, CG000238). Sections from four tissue blocks were placed on Visium Gene Expression slide for H&E staining and brightfield imaging via NanoZoomer SQ (Hamamatsu), block-specific tissue permeabilization, mRNA capture, and subsequent library generation per the manufacturer’s protocol (10x Genomics, CG000239).
Library concentration was quantified using a Tapestation High Sensitivity DNA ScreenTape (Agilent) and fluorometry (Thermofisher Qubit) and verified via KAPA qPCR. Libraries were pooled for sequencing on an Illumina NovaSeq 6000 using a 28-10-10-90 read configuration, targeting 100,000 read pairs per spot covered by tissue.
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
Description Flash frozen spatial transcriptome sequencing
Data processing Illumina base call files for all libraries were converted to FASTQs using bcl2fastq v2.20.0.422 (Illumina)
FASTQ files were split into mouse and human counterparts with Xenome 1.0.1
Mouse sequencing reads were aligned to mm10-2020-A genome with Space Ranger count 1.3.1
Human sequencing reads were aligned to GRCh38-2020-A genome with Space Ranger count 1.3.1
Human and mouse gene count matrices were merged into one matrix
Assembly: GRCh38 (GENCODE v32/Ensembl 98) and mm10 (GENCODE vM23/Ensembl 98)
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics
Submission date Jul 21, 2023
Last update date May 21, 2024
Contact name Jeffrey H Chuang
Organization name The Jackson Laboratory for Genomic Medicine
Street address 10 Discovery Drive
City Farmington
State/province CT
ZIP/Postal code 06032
Country USA
Platform ID GPL24247
Series (1)
GSE238004 Nextflow Pipeline for Visium and H&E Data from Patient-Derived Xenograft Samples
BioSample SAMN36678137
SRA SRX21125947

Supplementary file Size Download File type/resource
GSM7657719_SC2200094_aligned_fiducials.jpg.gz 1.2 Mb (ftp)(http) JPG
GSM7657719_SC2200094_barcodes.tsv.gz 25.3 Kb (ftp)(http) TSV
GSM7657719_SC2200094_detected_tissue_image.jpg.gz 1.8 Mb (ftp)(http) JPG
GSM7657719_SC2200094_features.tsv.gz 521.0 Kb (ftp)(http) TSV
GSM7657719_SC2200094_matrix.mtx.gz 36.2 Mb (ftp)(http) MTX
GSM7657719_SC2200094_scalefactors_json.json.gz 177 b (ftp)(http) JSON
GSM7657719_SC2200094_tissue_hires_image.png.gz 3.7 Mb (ftp)(http) PNG
GSM7657719_SC2200094_tissue_lowres_image.png.gz 313.5 Kb (ftp)(http) PNG
GSM7657719_SC2200094_tissue_positions_list.csv.gz 59.7 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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