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datasets_info
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datasets_info
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Human Prostate Cancer, Acinar Cell Carcinoma (FFPE)
Spatial Gene Expression Dataset by Space Ranger 1.3.0
5µm section from Acinar cell carcinoma of human prostate. FFPE tissue purchased from Indivumed Human Tissue Specimens (Indivumed).
Block 1D1061-Tp11 Section 1
Stage IV
Total Gleason score: 7
Magnification: 20x
Libraries were prepared following the Visium Spatial Gene Expression Reagent Kits for FFPE User Guide (CG000407 Rev A).
Sequenced on Illumina NovaSeq with approximately 50,207 reads per spot, dual index set SI-TS-B8, 28bp read 1 (16bp Visium spatial barcode, 12bp UMI), 50bp read2 (transcript), 10bp i7 sample barcode and 10bp i5 sample barcode.
FASTQ data were analyzed with Space Ranger 1.3. 3,043 spots detected under tissue. Annotated with Invasive Carcinoma.
https://www.10xgenomics.com/resources/datasets/human-prostate-cancer-acinar-cell-carcinoma-ffpe-1-standard
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Human Prostate Cancer, Adenocarcinoma with Invasive Carcinoma (FFPE)
Spatial Gene Expression Dataset by Space Ranger 1.3.0
5 µm section from Adenocarcinoma of Human Prostate. FFPE tissue purchased from Indivumed Human Tissue Specimens (Indivumed).
Block 1E500_Tp12 Section 1
Stage III
Total Gleason score: 7
Sex: Male
20x magnification
Libraries were prepared following the Visium Spatial Gene Expression Reagent Kits for FFPE User Guide (CG000407 Rev A).
Libraries were sequenced on Illumina NovaSeq with approximately 22,964 reads per spot, dual index set SI-TS-F8, 28bp read 1 (16bp Visium spatial barcode, 12bp UMI), 50bp read2 (transcript), 10bp i7 sample barcode and 10bp i5 sample barcode.
FASTQ data were analyzed with Space Ranger 1.3. 4371 spots were detected under tissue. Annotated with Adenocarcinoma, Invasive Carcinoma.
https://www.10xgenomics.com/resources/datasets/human-prostate-cancer-adenocarcinoma-with-invasive-carcinoma-ffpe-1-standard-1-3-0
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Human Prostate Cancer, Adjacent Normal Section with IF staining (FFPE)
Spatial Gene Expression Dataset by Space Ranger 1.3.0
10µm section from Adenocarcinoma of Human Prostate. FFPE tissue purchased from Indivumed Human Tissue Specimens (Indivumed). Original diagnosis with adenocarcinoma.
Block 1E333_Tp11 Section 1
Stage II
Total Gleason score: 7
Sex: Male
Antibodies used for immunofluorescence (IF) staining:
Channel 1 = 1:100 Iba1/AIF-1 (Cell Signalling, Cat. No. 36618S)
Channel 2 = 1:100 Vimentin (Cell Signalling, Cat. No. 9856S)
Channel 3 = 1:5000 DAPI (Thermo Scientific, Cat. No. 62248)
Blocking buffer: 1X PBS; 2% BSA; 0.1% Tween 20; 1 U/uL Roche Protector RNase Inhibitor (based on CoA)
Libraries were prepared following the Visium Spatial Gene Expression Reagent Kits for FFPE User Guide (CG000407 Rev A).
Sequenced on Illumina NovaSeq with dual index set SI-TS-D4, approximately 29,191 reads per spot. 28bp read 1 (16bp Visium spatial barcode, 12bp UMI), 50bp read2 (transcript), 10bp i7 sample barcode and 10bp i5 sample barcode.
FASTQ data were analyzed with Space Ranger 1.3. 3460 spots were detected under tissue using manual Loupe alignment.
https://www.10xgenomics.com/resources/datasets/human-prostate-cancer-adjacent-normal-section-with-if-staining-ffpe-1-standard-1-3-0
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Normal Human Prostate (FFPE)
Spatial Gene Expression Dataset by Space Ranger 1.3.0
5 µm section from human prostate. FFPE tissue purchased from Indivumed Human Tissue Specimens (Indivumed).
Block 1E333_Tn17
Sex: Male
Magnification: 20x
Libraries were prepared following the Visium Spatial Gene Expression Reagent Kits for FFPE User Guide (CG000407 Rev A).
Sequenced on Illumina NovaSeq with dual index set SI-TS-D2, approximately 27,893 reads per spot, 28bp read 1 (16bp Visium spatial barcode, 12bp UMI), 50bp read2 (transcript), 10bp i7 sample barcode and 10bp i5 sample barcode.
FASTQ data were analyzed with Space Ranger 1.3. 2539 spots detected under tissue.
https://www.10xgenomics.com/resources/datasets/normal-human-prostate-ffpe-1-standard-1-3-0
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