10x Genomics Visium Spatial Transcriptome
Mawonekedwe
● Kusamvana: 100 µM
● Spot Diameter: 55 µM
● Chiwerengero cha malo: 4992
● Malo ojambulidwa: 6.5 x 6.5 mm
● Malo aliwonse okhala ndi barcode amadzazidwa ndi zoyambira zomwe zili ndi magawo anayi:
- poly(dT) mchira wa mRNA priming ndi cDNA synthesis
- Unique Molecular Identifier (UMI) kuti akonze kukondera kokulitsa
- Barcode ya malo
- Kumangirira kowerengera pang'ono koyambira motsatizana
● Kudetsa kwa H & E kwa zigawo
Ubwino wake
●Utumiki woyima kamodzi: imaphatikiza zochitika zonse ndi masitepe otengera luso, kuphatikiza cryo-sectioning, staining, kukhathamiritsa kwa minofu, barcoding ya malo, kukonzekera laibulale, kutsatizana ndi bioinformatics.
● Aluso aluso gulu: Wodziwa zambiri pamitundu yopitilira 250 ya minofu ndi mitundu 100+ kuphatikiza anthu, mbewa, zoyamwitsa, nsomba ndi zomera.
●Zosintha zenizeni za polojekiti yonse: ndi ulamuliro wonse wa kupita patsogolo kwa kuyesera.
●Comprehensive standard bioinformatics:phukusi limaphatikizapo 29 kusanthula ndi 100+ ziwerengero zapamwamba.
●Kusanthula kwatsatanetsatane ndikuwona mawonekedwe: kupezeka pazofunsitsa zosiyanasiyana.
●Kusanthula kophatikizana kosankha ndi katsatidwe ka One-cell mRNA
Zofotokozera
| Zitsanzo Zofunika | Library | Njira yotsatirira | Deta yovomerezeka | Kuwongolera Kwabwino |
| Zitsanzo za cryo zophatikizidwa ndi OCT, zitsanzo za FFPE (M'mimba mwake mulingo woyenera: pafupifupi 6x6x6 mm3) 3 midadada pa chitsanzo | 10X Visium cDNA library | Chithunzi cha PE150 | 50K PE imawerengedwa pa malo (60Gb) | RIN> 7 |
Kuti mumve zambiri zachitsogozo chokonzekera zitsanzo ndi kayendedwe ka ntchito, chonde omasuka kulankhula ndi aBMKGENE katswiri
Njira ya utumiki
Mu gawo lokonzekera lachitsanzo, kuyesa koyambirira kwa RNA kochulukira kumachitika kuti zitsimikizire kuti RNA yapamwamba kwambiri ingapezeke.Mu gawo la kukhathamiritsa kwa minofu zigawozo zimadetsedwa ndikuwonetseredwa komanso momwe permeabilization yotulutsa mRNA kuchokera ku minofu imakongoletsedwa.Protocol yokhathamiritsa imagwiritsidwa ntchito pomanga laibulale, ndikutsatiridwa ndi kutsata ndi kusanthula deta.
Kuyenda kwathunthu kwautumiki kumaphatikizapo zosintha zenizeni zenizeni ndi kutsimikizika kwamakasitomala kuti mukhalebe ndi mayankho omvera, kuwonetsetsa kuti polojekiti ichitike bwino.
Mulinso zowunikira izi:
Kuwongolera Ubwino wa Data:
o Kutulutsa kwa data ndi kugawa kwamagulu abwino
o Kuzindikira majini pa malo
o Kufalikira kwa minofu
Kusanthula kwachitsanzo chamkati:
o Kulemera kwa majini
o Kuphatikizika kwamadontho, kuphatikiza kuwunika kwafupipafupi
o Kusanthula kwamafotokozedwe osiyanasiyana pakati pa magulu: kuzindikira jini zolembera
o Kafotokozedwe ka ntchito komanso kukulitsa ma jini olembera
Kusanthula kwamagulu
o Kuphatikizanso mawanga kuchokera ku zitsanzo zonse (monga matenda ndi kuwongolera) ndikuphatikizanso
o Kuzindikiritsa jini zolembera pagulu lililonse
o Kafotokozedwe ka ntchito komanso kukulitsa ma jini olembera
o Kusiyanitsa kwa gulu limodzi pakati pa magulu
Kusanthula kwachitsanzo chamkati
Spot clustering
Chizindikiritso cha majini a chikhomo ndi kugawa kwamalo
Inter-group Analysis
Kuphatikiza deta kuchokera m'magulu onse awiri ndikuphatikizanso
Ma jini olembera magulu atsopano
Onani kupita patsogolo komwe kumayendetsedwa ndi BMKGene's spatial transcriptomics service yolembedwa ndi 10X Visium M'mabuku awa:
Chen, D. et al.(2023) 'mthl1, kuthekera kwa Drosophila homologue of mammalian adhesion GPCRs, akukhudzidwa ndi zochita za antitumor ku ma cell a oncogenic mu ntchentche', Proceedings of the National Academy of Sciences of the United States of America, 120(30), p.e2303462120.doi: /10.1073/pnas.2303462120
Chen, Y. et al.(2023) 'STEEL imathandizira kutanthauzira kwakukulu kwa data ya spatiotemporal transcriptomic', Briefings in Bioinformatics, 24 (2), pp. 1-10.doi: 10.1093/BIB/BBAD068.
Liu, C. et al.(2022) 'Spatiotemporal atlas of organogenesis mu chitukuko cha maluwa a orchid', Nucleic Acids Research, 50 (17), pp. 9724-9737.doi: 10.1093/NAR/GKAC773.
Wang, J. et al.(2023) 'Integrating Spatial Transcriptomics ndi Single-nucleus RNA Sequencing Iwulula Njira Zomwe Zingatheke Zochizira Uterine Leiomyoma', International Journal of Biological Sciences, 19 (8), pp. 2515-2530.doi: 10.7150/IJBS.83510.
