BMKMANU S1000 Spatial Transcriptome
BMKMANU S1000 Spatial Transcriptome Technical Scheme
Nta
● Kev daws teeb meem: 5 µM
● Spot Diameter: 2.5 µM
● Tus naj npawb ntawm qhov chaw: kwv yees li 2 lab
● 3 lub peev xwm capture cheeb tsam hom: 6.8 mm * 6.8 mm, 11 mm * 11 mm los yog 15 mm * 20 mm
● Txhua lub hlaws barcoded yog loaded nrog primers muaj li ntawm 4 seem:
poly (dT) tail rau mRNA priming thiab cDNA synthesis
Unique Molecular Identifier (UMI) los kho qhov kev hloov pauv tsis zoo
Spatial barcode
Binding sequence ntawm ib feem nyeem 1 sequencing primer
● H&E thiab fluorescent staining ntawm seem
● Muaj peev xwm siv taucell segmentation technology: Kev sib koom ua ke ntawm H&E staining, fluorescent staining, thiab RNA sequencing los txiav txim txog thaj tsam ntawm txhua lub xovtooj thiab muab cov gene qhia rau txhua lub cell.
Qhov zoo ntawm BMKMANU S1000
●Sub-cellular daws teeb meem: Txhua qhov chaw ntes muaj> 2 lab spatial Barcoded Spots nrog txoj kab uas hla ntawm 2.5 µm thiab qhov sib nrug ntawm 5 µm ntawm qhov chaw, ua kom muaj kev soj ntsuam spatial transcriptome nrog sub-cellular daws teeb meem (5 µm).
●Multi-level Resolution Analysis:Kev txheeb xyuas ntau theem sib txawv ntawm 100 μm mus rau 5 μm los daws cov ntaub so ntswg sib txawv ntawm qhov kev daws teeb meem zoo.
● Muaj peev xwm siv "Peb hauv ib qho swb" Cell Segmentation Technology:Ua ke fluorescence staining, H&E staining, thiab RNA sequencing ntawm ib tug swb, peb "peb-hauv-ib" tsom xam algorithm txhawb kev txheeb xyuas ntawm cov ciam teb ntawm tes rau cov cell-based transcriptomics tom ntej.
●Tau tshaj Multiple Sequencing Platforms: Ob leeg NGS thiab cov ntawv nyeem ntev ntev muaj.
●Saj zawg zog tsim ntawm 1-8 Active Capture Area: Qhov luaj li cas ntawm qhov chaw ntes yog hloov tau, siv tau 3 hom (6.8mm * 6.8mm., 11mm * 11mm thiab 15mm * 20mm)
●One-stop Service: Nws koom ua ke 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.
●Comprehensive Bioinformatics thiab User-friendly Visualization of Results:pob suav nrog 29 kev tshuaj xyuas thiab 100+ cov duab zoo, ua ke nrog kev siv cov software tsim hauv tsev kom pom thiab kho cov cell splitting thiab qhov chaw sib cais.
●Customized Data Analysis thiab Visualization: muaj rau kev tshawb nrhiav sib txawv
●Pab neeg ua haujlwm siab heev: nrog kev paub dhau 250 hom ntaub so ntswg thiab 100+ hom nrog rau tib neeg, nas, tsiaj txhu, ntses thiab nroj tsuag.
●Real-time Updates ntawm Tag Nrho Cov Haujlwm: nrog kev tswj tag nrho ntawm kev sim ua tiav.
●Kev Tshawb Fawb Kev Sib Koom Nrog Ib leeg-cell mRNA Sequencing
Service Specifications
|
Qauv Kev xav tau
| Lub tsev qiv ntawv |
Sequencing tswv yim
| Cov ntaub ntawv pom zoo | Kev Tswj Xyuas Zoo |
| OCT-embedded cryo qauv, 3 blocks ib qho qauv | S1000 cDNA qiv | Illumina PE150 (lwm lub platform muaj) | 100K PE nyeem ib 100 uM (60-150 Gb) | 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 Flow
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.
Cov ntaub ntawv tsim los ntawm BMKMANU S1000 yog tshuaj xyuas siv software "BSTMatrix", uas yog tus kheej tsim los ntawm BMKGENE, tsim cov Gene Expression Matrix. Los ntawm qhov ntawd, ib daim ntawv tshaj tawm tus qauv raug tsim tawm uas suav nrog kev tswj xyuas cov ntaub ntawv zoo, kev tshuaj xyuas sab hauv-piv txwv thiab kev txheeb xyuas cov pab pawg.
● Data Quality Control:
Cov ntaub ntawv tso tawm thiab kev faib cov qhab nia zoo
Gene detection ib qhov chaw
Cov ntaub so ntswg npog
● Inner-piv txwv tsom xam:
Gene nplua nuj
Spot clustering, suav nrog txo qhov ntsuas qhov ntsuas
Kev txheeb xyuas qhov sib txawv ntawm cov pawg: txheeb xyuas cov cim cim
Functional annotation thiab enrichment ntawm marker noob
● Kev tsom xam Inter-pab pawg:
Kev sib xyaw ua ke ntawm cov pob los ntawm ob qho tib si kuaj (xws li kab mob thiab kev tswj hwm) thiab rov ua pawg
Kev txheeb xyuas cov cim cim rau txhua pawg
Functional annotation thiab enrichment ntawm marker noob
Differential Qhia ntawm tib pawg ntawm pawg
Tsis tas li ntawd, BMKGENE tau tsim "BSTViewer" yog cov cuab yeej siv tau zoo uas ua rau tus neeg siv pom cov noob qhia thiab pom qhov sib txawv ntawm cov kev daws teeb meem sib txawv.
BMKGene tsim software rau cov neeg siv tus phooj ywg pom kev pom
BSTViewer qhov chaw sib cais ntawm ntau theem daws teeb meem
BSTcellViewer: tsis siv neeg thiab phau ntawv tes splitting
Inner-sample Analysis
Spot clustering:
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 genes ntawm pawg tshiab:
Tshawb nrhiav cov kev nce qib uas tau pab los ntawm BMKGene cov kev pabcuam spatial transcriptomics nrog BMKManu S1000 thev naus laus zis hauv cov ntawv tshaj tawm no:
Song, X. et al. (2023) 'Spatial transcriptomics nthuav tawm lub teeb-induced chlorenchyma hlwb koom nrog hauv kev txhawb nqa tua rov tsim dua hauv lws suav callus',Cov txheej txheem ntawm National Academy of Sciences ntawm Tebchaws Meskas, 120(38), p. ib 2310163120. doi: 10.1073/pnas.2310163120 ib
Koj, Y. et al. (2023) 'Systematic sib piv ntawm sequencing-based spatial transcriptomic method',bioRxiv,ua p. 2023.12.03.569744 ib. doi: 10.1101/2023.12.03.569744 ib.
