10x Genomics Visium Spatial Transcriptome
Nta
● Kev daws teeb meem: 100 µM
● Spot Diameter: 55 µM
● Tus naj npawb ntawm qhov chaw: 4992
● Capture cheeb tsam: 6.5 x 6.5 mm
● Txhua qhov chaw barcoded yog loaded nrog primers muaj li ntawm 4 seem:
- poly (dT) tail rau mRNA priming thiab cDNA synthesis
- Cim Molecular Identifier (UMI) los kho qhov kev hloov pauv tsis zoo
- Spatial barcode
- Kev sib txuas ua ke ntawm ib feem nyeem 1 sequencing primer
● H&E staining ntawm seem
Qhov zoo
●Kev pabcuam ib-nres: integrates tag nrho cov kev paub dhau los thiab cov kev txawj raws li cov kauj ruam, suav nrog cryo-sectioning, staining, cov ntaub so ntswg optimization, spatial barcoding, npaj tsev qiv ntawv, sequencing thiab bioinformatics.
● Pab neeg muaj kev txawj ntse heev: nrog kev paub dhau 250 hom ntaub so ntswg thiab 100+ hom nrog rau tib neeg, nas, tsiaj txhu, ntses thiab nroj tsuag.
●Lub sijhawm hloov tshiab ntawm tag nrho qhov project: nrog kev tswj tag nrho ntawm kev sim ua tiav.
●Comprehensive standard bioinformatics:pob suav nrog 29 kev tshuaj xyuas thiab 100+ cov duab zoo.
●Customized data analysis thiab visualization: muaj rau kev tshawb nrhiav sib txawv.
●Kev xaiv kev sib koom ua ke nrog ib leeg-cell mRNA sequencing
Specifications
| Cov Qauv Xav Tau | Lub tsev qiv ntawv | Sequencing tswv yim | Cov ntaub ntawv pom zoo | Kev Tswj Xyuas Zoo |
| OCT-embedded cryo qauv, FFPE cov qauv (Qhov zoo tshaj plaws txoj kab uas hla: approx. 6x6x6 mm3) 3 blocks rau ib qho qauv | 10X Visium cDNA tsev qiv ntawv | Illumina PE 150 | 50K PE nyeem ib qhov chaw (60Gb) | RIN> 7 |
Yog xav paub ntxiv txog cov qauv qhia kev npaj thiab kev pabcuam kev ua haujlwm, thov koj tham nrog aBMKGENE tus kws tshaj lij
Kev Pabcuam Ua Haujlwm
Hauv theem kev npaj ua qauv, thawj zaug RNA rho tawm mus sim yog ua kom ntseeg tau tias RNA zoo tuaj yeem tau.Nyob rau hauv cov ntaub so ntswg optimization theem cov seem yog stained thiab visualized thiab permeabilization tej yam kev mob rau mRNA tso tawm ntawm cov ntaub so ntswg yog optimized.Cov txheej txheem optimized yog tom qab ntawd siv thaum lub sij hawm tsim tsev qiv ntawv, ua raws li kev sib txuas thiab kev txheeb xyuas cov ntaub ntawv.
Kev ua haujlwm tiav kev pabcuam suav nrog kev hloov kho lub sijhawm tiag tiag thiab cov neeg siv khoom lees paub los tswj cov lus teb cov lus teb, kom ntseeg tau tias kev ua tiav txoj haujlwm zoo.
Xws li cov kev txheeb xyuas hauv qab no:
Data Quality Control:
o Cov ntaub ntawv tso tawm thiab kev faib cov qhab nia zoo
o Kev txheeb xyuas cov noob rau ib qho chaw
o Cov ntaub so ntswg npog
Inner-sample tsom xam:
o Gene nplua nuj
o Spot clustering, suav nrog txo qhov ntsuas qhov ntsuas
o Kev txheeb xyuas qhov sib txawv ntawm pawg: kev txheeb xyuas cov cim cim
o Cov lus piav qhia ua haujlwm thiab ua kom muaj txiaj ntsig ntawm cov cim cim
Inter-pab pawg tsom xam
o Kev sib xyaw ua ke ntawm cov pob los ntawm ob qho qauv (xws li kab mob thiab kev tswj hwm) thiab rov ua pawg
o Kev txheeb xyuas cov cim cim rau txhua pawg
o Cov lus piav qhia ua haujlwm thiab ua kom muaj txiaj ntsig ntawm cov cim cim
o Qhov txawv ntawm qhov sib txawv ntawm tib pawg ntawm pawg
Inner-sample Analysis
Kev sib koom ua ke
Kev txheeb xyuas cov noob caj noob ces thiab spatial faib
Inter-group Analysis
Cov ntaub ntawv sib xyaw los ntawm ob pawg thiab rov ua pawg
Marker noob ntawm pawg tshiab
Tshawb nrhiav cov kev nce qib uas tau pab los ntawm BMKGene qhov kev pabcuam spatial transcriptomics los ntawm 10X Visium Hauv cov ntawv tshaj tawm tshwj xeeb no:
Chen, D. et al.(2023) 'mthl1, muaj peev xwm Drosophila homologue ntawm mammalian adhesion GPCRs, yog koom nrog cov tshuaj tiv thaiv kab mob rau cov kab mob oncogenic hauv yoov', Kev Ua Haujlwm ntawm National Academy of Sciences ntawm Tebchaws Meskas, 120(30), p.ib 2303462120.doi: /10.1073/pnas.2303462120
Chen, Y. et al.(2023) 'STEEL enables high-resolution delineation of spatiotemporal transcriptomic data', Briefings in Bioinformatics, 24(2), pp. 1–10.doi: 10.1093/BIB/BBAD068.
Liu, C. et al.(2022) 'A spatiotemporal atlas of organogenesis nyob rau hauv kev loj hlob ntawm orchid paj', Nucleic Acids Research, 50(17), pp. 9724–9737.doi: 10.1093/NAR/GKAC773.
Wang, J. et al.(2023) 'Integrating Spatial Transcriptomics and Single-nucleus RNA Sequencing Reveals the Potential Therapeutic Strategies for Uterine Leiomyoma', International Journal of Biological Sciences, 19(8), pp. 2515–2530.doi: 10.7150/IJBS.83510.
