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| Status |
Public on Dec 01, 2023 |
| Title |
Treat_1 |
| Sample type |
SRA |
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| Source name |
Cal27
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Cal27
cell type: Human oral cell line
donor: purchased from ATCC
culture time: 6h
treatment: BSArGO@ZIF-8 NSs
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| Treatment protocol |
Cells were treated with BSArGO@ZIF8 NSs at a multiplicity of infection (MOI) of F. nucleatum : cell =10:1, and culured at 3d, 7d, 14d and 21d
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| Growth protocol |
Cells were cultured with 6-well plates at 37°C in a humidified atmosphere of 5% CO2.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated, evaluated the quality, reverse-transcribed to cDNA,
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
Genome_build: hg38
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| Submission date |
Dec 17, 2021 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Wenyan Kang |
| E-mail(s) |
202090000024@sdu.edu.cn
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| Organization name |
Shandong university
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| Street address |
No. 44-1 Wenhua Road West
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| City |
Jinan, Shandong |
| ZIP/Postal code |
250012 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE191172 |
In situ Growth of ZIF-8 Nanoparticles on Graphene Oxide Nanosheets: A Multifunctional Nanoplatform for Combined Ion‐interference and Photothermal Therapy |
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| Relations |
| BioSample |
SAMN24173980 |
| SRA |
SRX13442791 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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