|
| Status |
Public on May 21, 2024 |
| Title |
WM4237-1, mouse 1337, untreated, sample S1 |
| 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 |
| E-mail(s) |
jeff.chuang@jax.org
|
| 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 |
|
| Relations |
| BioSample |
SAMN36678139 |
| SRA |
SRX21125945 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7657717_SC2200092_aligned_fiducials.jpg.gz |
1.1 Mb |
(ftp)(http) |
JPG |
| GSM7657717_SC2200092_barcodes.tsv.gz |
25.3 Kb |
(ftp)(http) |
TSV |
| GSM7657717_SC2200092_detected_tissue_image.jpg.gz |
1.8 Mb |
(ftp)(http) |
JPG |
| GSM7657717_SC2200092_features.tsv.gz |
521.0 Kb |
(ftp)(http) |
TSV |
| GSM7657717_SC2200092_matrix.mtx.gz |
29.4 Mb |
(ftp)(http) |
MTX |
| GSM7657717_SC2200092_scalefactors_json.json.gz |
180 b |
(ftp)(http) |
JSON |
| GSM7657717_SC2200092_tissue_hires_image.png.gz |
3.5 Mb |
(ftp)(http) |
PNG |
| GSM7657717_SC2200092_tissue_lowres_image.png.gz |
297.2 Kb |
(ftp)(http) |
PNG |
| GSM7657717_SC2200092_tissue_positions_list.csv.gz |
60.7 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
