10x Genomics Visium Spatial Transcriptome
Features
● Kugadziriswa: 100 µM
● Spot Diameter: 55 µM
● Nhamba yenzvimbo: 4992
● Kutora nzvimbo: 6.5 x 6.5 mm
● Nzvimbo yega yega ine barcode yakatakurwa neprimers inoumbwa nezvikamu zvina:
- poly(dT) muswe wemRNA priming uye cDNA synthesis
-Unique Molecular Identifier (UMI) kugadzirisa kusarura kwekusimudzira
- Spatial barcode
-Kusunga kutevedzana kwechidimbu kuverenga 1 kutevedzana kwekutanga
● H & E kusvibiswa kwezvikamu
Zvakanakira
●One-stop service: inobatanidza zvese ruzivo uye hunyanzvi-hwakavakirwa matanho, kusanganisira cryo-chikamu, kusvibisa, optimization yetishu, spatial barcoding, kugadzirira raibhurari, kutevedzana uye bioinformatics.
● Chikwata chehunyanzvi chehunyanzvi: ine ruzivo mumhando dzinopfuura mazana maviri nemakumi mashanu emhando dzematishu uye 100+ mhando dzinosanganisira vanhu, mbeva, zvinoyamwisa, hove uye zvidyarwa.
●Real-time update pane yese purojekiti: nekutonga kwakazara kwekufambira mberi kwekuedza.
●Yakakwana yakajairika bioinformatics:pasuru inosanganisira 29 ongororo uye 100+ yepamusoro-mhando nhamba.
●Customized data kuongorora uye kuona: inowanikwa kune zvakasiyana zvikumbiro zvekutsvaga.
●Optional joint analysis neSingle-cell mRNA sequencing
Zvinotsanangurwa
| Mienzaniso Zvinodiwa | Library | Sequencing strategy | Data inokurudzirwa | Quality Control |
| OCT-yakaiswa cryo samples, FFPE samples (Yakanyanya kureba: approx. 6x6x6 mm3) 3 zvidhinha pamuenzaniso | 10X Visium cDNA raibhurari | Illumina PE150 | 50K PE inoverenga pane imwe nzvimbo ( 60Gb ) | RIN>7 |
Kuti uwane rumwe ruzivo nezve nhungamiro yegadziriro yemuenzaniso uye mafambiro ebasa, ndapota inzwa wakasununguka kutaura kune aBMKGENE nyanzvi
Service Workflow
Muchikamu chekugadzirira chemuenzaniso, yekutanga kuwanda kweRNA kutorwa kuyedzwa kunoitwa kuti ive nechokwadi chekuti RNA yemhando yepamusoro inogona kuwanikwa.Muchikamu chekugadzirisa matishu zvikamu zvakasvibiswa uye zvinoonekwa uye mamiriro epermeabilization ekuburitswa kwemRNA kubva munyama anogadziriswa.Iyo yakagadziridzwa protocol inozoshandiswa panguva yekuvaka raibhurari, ichiteverwa nekutevedzana uye kuongororwa kwedata.
Iyo yakazara sevhisi kufambiswa kwebasa kunosanganisira chaiyo-nguva yekuvandudza uye kusimbiswa kwevatengi kuchengetedza inopindura mhinduro loop, kuve nechokwadi chekuita kwakatsetseka kweprojekiti.
Inosanganisira ongororo inotevera:
Data Quality Control:
o Kubuda kwedata uye kugovera zvibodzwa zvemhando
o Kuonekwa kwemajini pane imwe nzvimbo
o Kuvharwa kwenyama
Yemukati-sample wongororo:
o Gene kupfuma
o Spot clustering, kusanganisira yakaderedzwa dimension analysis
o Kuongororwa kwekutaura kwakasiyana pakati pemasumbu: kuzivikanwa kwemakina magene
o Inoshanda tsinhiro uye hupfumi hwemaka gene
Inter-group analysis
o Kubatanidzwazve kwemavara kubva kune ese masampuli (semuenzaniso. ane chirwere uye kutonga) uye kubatanidza zvakare
o Kuzivikanwa kwemajini emakaki kusumbu rega rega
o Inoshanda tsinhiro uye hupfumi hwemaka gene
o Musiyano Kuratidzwa kwesumbu rimwechete pakati pemapoka
Inner-sample Analysis
Spot clustering
Mucherechedzo wemajini uye kugovera kwenzvimbo
Inter-group Analysis
Musanganiswa wedata kubva kumapoka maviri uye re-cluster
Marker majini emasumbu matsva
Ongorora kufambira mberi kwakafambiswa neBMKGene's spatial transcriptomics sevhisi ne10X Visium Mune aya akanyorwa zvinyorwa:
Chen, D. et al.(2023) 'mthl1, inogona Drosophila homologue ye mammalian adhesion GPCRs, inobatanidzwa mukuita antitumor kune jekiseni oncogenic masero munhunzi', Proceedings of the National Academy of Sciences yeUnited States of America, 120 (30), p.e2303462120.doi: /10.1073/pnas.2303462120
Chen, Y. et al.(2023) 'STEEL inogonesa yakakwirira-resolution delineation yespatiotemporal transcriptomic data', Pfupiso muBioinformatics, 24 (2), mapeji 1-10.doi: 10.1093/BIB/BBAD068.
Liu, C. nevamwe.(2022) 'Aspatiotemporal atlas ye organogenesis mukugadzirwa kwemaruva eorchid', Nucleic Acids Research, 50 (17), mapeji 9724-9737.doi: 10.1093/NAR/GKAC773.
Wang, J. nevamwe.(2023) 'Kubatanidza Spatial Transcriptomics uye Single-nucleus RNA Sequencing Inozivisa Ingangove Yekurapa Matanho eUterine Leiomyoma', International Journal yeBiological Sayenzi, 19 (8), mapeji 2515-2530.doi: 10.7150/IJBS.83510.
