Human Cervical Cancer (FFPE)
Dataset ID: STDS0000113
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2,781 Spots
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17,943 Genes
Catalog
Dataset information
Contributors
Accessions
Dataset information
Summary:
5 µm section from squamous cell carcinoma of human cervical cancer. FFPE tissue purchased from Discovery Life Sciences. Block C00084155.1a Cervical Cancer, Invasive. Squamous cell carcinoma T1bN0M0 IB Brightfield camera, Magnification: 20x Sequencing instrument: Illumina NovaSeq 6000, flow cell HVFG7DSXY (lanes 1-4) Sequencing depth: 72,087 reads per spot Sequencing configuration: 28 bp read 1 (16 bp Visium spatial barcode, 12 bp UMI), 50 bp read 2 (transcript), 10 bp i7 sample barcode and 10 bp i5 sample barcode Dual-Index set: SI-TS-E5 Slide: V10L13-019 Area: A1 This dataset is licensed under the Creative Commons Attribution license.
Overall design:
A single human reference nephrectomy (female aged 59 without histologic evidence of kidney disease) was acquired from the Biopsy Biobank Cohort of Indiana (BBCI). From age-matched 8-10 week old 129/ SvEv mice (Taconic Biosciences, Albany, New York), tissues were acquired from a sham mouse in which the abdomen was opened and sutured back and mice which underwent ischemia-reperfusion injury (IRI) or cecal ligation and puncture (CLP). In the IRI model both renal pedicles were exposed and clamped for 22 minutes through a midline incision then released. In the CLP model, the cecum was ligated and punctured with a 25 gauge needle. Kidneys were excised upon sacrifice 6 hours after each procedure and frozen in Optimal Cutting Temperature (OCT) compound. Slide preparation (CG000240_Demonstrated_Protocol_VisiumSpatialProtocols_TissuePreparationGuide_Rev_A, 10X Genomics), imaging (CG000241_VisiumImagingGuidelinesTN_Rev_A, 10X Genomics), mRNA extraction, library preparation, and sequencing (CG000239_VisiumSpatialGeneExpression_UserGuide_RevD, 10X Genomics) were conducted according to Visium Spatial Gene Expression protocols . Frozen transverse 10 碌m sections from the human nephrectomy or each murine model were placed within the etched frames of the capture areas on the active surface of the Visium Spatial Slide. Tissue sections were fixed in methanol and stained with hematoxylin and eosin (H&E). Stained tissue sections were permeabilized for 12 minutes, and the cDNA libraries were prepared and sequenced on an Illumina NovaSeq 6000 with 28bp+120bp paired-end sequencing mode.
Technology:
10x Visium
Platform:
Illumina NovaSeq 6000
Species:
Homo sapiens(hg38)
Tissues:
Cervical
Organ parts:
Cervical cancer
Cell types:
squamous cell
Disease:
Cervical cancer
Submission date: 2020-03-29Update date: 2020-03-29
Sample number: 1Section number: 1
Contributors
Eadon Michael; Ricardo Melo Ferreira; Ying-Hua Cheng
Accessions
10x visium data: 10x GENOMICS