BMKMANU S3000_Spatial Transcriptome
BMKMANU S3000 Spatial Transcriptome Technical Scheme
Features
- Kugadziriswa: 3.5 μM
- Spot Diameter: 2.5 µM
- Nhamba yenzvimbo: ingangoita 4 Mamirioni
- 3 inobvira yekutora nzvimbo mafomati: 6.8 mm * 6.8 mm, 11 mm * 11 mm kana 15 mm * 20 mm
- Imwe neimwe barcode bead inoremerwa neprimers inoumbwa nezvikamu zvina:
• poly(dT) muswe wemRNA priming uye cDNA synthesis,
• Unique Molecular Identifier (UMI) kugadzirisa kusarerekera kweamplification
• Spatial barcode
• Kusunga kutevedzana kwechikamu verenga 1 kutevedzana kwekutanga
- H&E uye fluorescent staining yezvikamu
-Kugona kushandisa sero segmentation tekinoroji: kubatanidzwa kweH&E kusvibisa, fluorescent staining, uye RNA sequencing kuona miganhu yesero rega rega uye nenzira kwayo kugovera gene kutaura kune yega yega. Kugadzirisa kudzika kweSpatial profiling ongororo yakavakirwa pasero bhini.
-Inogoneka kuwana multilevel resolution yekuongorora: Flexible multi-level kuongororwa kubva ku100um kusvika 3.5 um kugadzirisa akasiyana matishu maficha pakugadziriswa kwakanyanya.
Zvakanakira zveBMKMANU S3000
-Kupetwa kaviri kwenzvimbo dzekutora kusvika ku4 Mamirioni: ine yakagadziridzwa resolution ye3.5 uM, inotungamira kune yakakwira gene uye UMI yekuona pasero. Izvi zvinokonzeresa kuunganidzwa kwakavandudzwa kwemaseru zvichibva pane zvinyorwa zvinyorwa, zvine ruzivo rwakakwana rwunoenderana nechimiro chematishu.
- Sub-cellular resolution:Imwe neimwe nzvimbo yekutora yaive ne> 2 miriyoni spatial Barcoded Spots ine dhayamita ye2.5 µm uye nzvimbo ye5 µm pakati penzvimbo dzemavara, ichigonesa spatial transcriptome kuongororwa ne sub-cellular resolution (5 µm).
-Multi-level resolution analysis:Flexible multi-level ongororo kubva ku100 μm kusvika 5 μm kugadzirisa akasiyana matishu maficha pakugadziriswa kwakaringana.
-Kugona kushandisa "Matatu mune imwe slide" maseru segmentation tekinoroji:kusanganisa fluorescence staining, H&E staining, uye RNA kutevedzana pane imwechete siraidhi, yedu "matatu-mu-imwe" yekuongorora algorithm inogonesa kuzivikanwa kwesero miganhu yeanotevera cell-based transcriptomics.
-Inopindirana nemapuratifomu akawanda ekutevedzana: zvese NGS uye yakareba-yekuverenga kutevedzana iripo.
-Flexible dhizaini ye1-8 inoshanda yekubata nzvimbo: saizi yenzvimbo yekutora inochinjika, zvichikwanisika kushandisa 3 mafomati (6.8 mm * 6.8 mm., 11 mm * 11 mm uye 15 mm * 20 mm)
-One-stop service: Inobatanidza zvese ruzivo uye hunyanzvi-hwakavakirwa matanho, kusanganisira cryo-chikamu, kusvibisa, optimization yetishu, spatial barcoding, kugadzirira raibhurari, kutevedzana, uye bioinformatics.
-Yakakwana bioinformatics uye mushandisi-ane hushamwari kuona kwemhedzisiro:Pasuru inosanganisira makumi maviri nemapfumbamwe ekuongorora uye 100+ yemhando yepamusoro nhamba, yakasanganiswa nekushandiswa kweiyo inhouse yakagadziridzwa software yekuona uye kugadzirisa kupatsanurwa kwesero uye kubatanidza nzvimbo.
-Customized data kuongorora uye kuona: inowanikwa kune zvakasiyana zvikumbiro zvekutsvaga
-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 inogadziridza pane yese purojekiti: nekutonga kwakazara kwekufambira mberi kwekuedza.
-Optional joint analysis neSingle-cell mRNA sequencing
Sevhisi Zvinotsanangurwa
| Muenzaniso Zvinodiwa | Library | Sequencing Strategy | Data Recommended | Quality Control |
| OCT-yakaiswa cryo samples (Yakakwana dhayamita: approx. 6×6×6mm³) 2 zvidhinha pamuenzaniso 1 yekuyedza, 1 ye backup | S3000 cDNA Library | Illumina PE150 | 160K PE inoverengwa pa100υM (250 Gb) | RIN > 7 |
Kuti uwane rumwe ruzivo nezve nhungamiro yegadziriro yemuenzaniso uye mafambiro ebasa, ndapota inzwa wakasununguka kutaura kune aBMKGENE nyanzvi
Kuyerera Kwebasa Rebasa
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.
Iyo data yakagadzirwa neBMKMANU S3000 inoongororwa uchishandisa software "BSTMatrix", iyo yakazvimiririra yakagadzirwa neBMKGENE, ichigadzira sero level uye multilevel resolution Gene Expression Matrix. Kubva ipapo, mushumo wakajairika unogadzirwa unosanganisira kutonga kwemhando yedata, kuongorora kwemukati-sample uye kuongororwa kweboka.
-Kudzora Hunhu hweData:
-Kubuda kwedata uye kugovera kwemhando yepamusoro
-Kuonekwa kwegene pane imwe nzvimbo
- Kufukidzwa kwetishu
- Yemukati-sample ongororo:
- Gene kupfuma
- Spot clustering, kusanganisira yakaderedzwa dimension kuongororwa
-Kuongorora kwakasiyana kwekutaura pakati pemasumbu: kuzivikanwa kwemakina majini
-Inoshanda tsinhiro uye hupfumi hwemaka gene
- Inter-group analysis
-Kusanganiswazve kwemavara kubva kumasamples ese ari maviri (semuenzaniso, kurwara nekudzora) uye kubatanidza zvakare
-Kuzivikanwa kwemakina emajini kune yega yega sumbu
-Inoshanda tsinhiro uye hupfumi hwemaka gene
-Musiyano Kuratidzwa kweboka rimwechete pakati pemapoka
Pamusoro pezvo, iyo BMKGene yakagadziridzwa "BSTViewer" chishandiso chine mushandisi-chinogonesa mushandisi kuona mataurirwo ejini uye kuungana kwemavara pazvisarudzo zvakasiyana.
BMKGene inopa spatial profiling masevhisi pane chaiyo-sero resolution (zvichienderana nesero bhini kana multilevel sikweya bhini kubva pa100um kusvika 3.5um).
Spatial profiling data kubva pamatishu zvikamu paS3000 siraidhi yakaitwa nemazvo sezviri pazasi.
Nyaya yechidzidzo 1: Uropi hwembeva
Kuongororwa kwechikamu cheuropi chembeva neS3000 kwakaguma nekuzivikanwa kwe ~ 94 000 masero, nekutevedzana kwepakati kwe ~ 2000 majini pasero. Kugadziriswa kwakavandudzwa kwe3.5 uM kwakakonzera kuunganidzwa kwakadzama kwemaseru kwakavakirwa pamatanho ekunyora, nemasumbu emasero anoteedzera uropi hwakapatsanurwa zvimiro. Izvi zvinoonekwa zviri nyore nekuona kugoverwa kwemasero akaungana se oligodendrocytes uye microglia masero, ayo anenge ari oga anowanikwa mune grey uye chena nyaya, zvichiteerana.
Nyaya yechidzidzo 2: Mbeva embryo
Ongororo yechikamu chembeva yembeva ine S3000 yakakonzera kuzivikanwa kwe ~ 2200 000 masero, nekutevedzana kwepakati kwe ~ 1600 majini pasero. Kugadziriswa kwakagadziridzwa kwe3.5 uM kwakakonzera kuunganidzwa kwakadzama kwemasero kwakavakirwa pamatanho ezvinyorwa, aine masumbu gumi nemaviri munzvimbo yeziso uye 28 masumbu munzvimbo yehuropi.
Inner-sample Analysis Cell clustering:
Kuzivikanwa kwemajini emakaki uye kugovera kwenzvimbo:
- yakakwira sub-cellular resolution: Kuenzaniswa neS1000 slide, imwe neimwe yekutora nzvimbo yeS3000 yaive > 4 miriyoni spatial Barcoded Spots ine dhayamita ye2.5 µm uye chinhambwe che3.5 µm pakati penzvimbo dzemavara, ichigonesa spatial transcriptome kuongororwa nepamusoro sub-cellular resolution (square bhini: 3.5 µm).
-Kunyanya kubatwa zvakanaka: zvichienzaniswa neS1000 slide, Median_UMI inowedzera kubva pa30% kusvika 70%, Median_Gene inowedzera kubva pa30% kusvika 60%
Chirongwa cheS1000 chip:
Chirongwa cheS3000 chip:
