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Status |
Public on Jul 23, 2024 |
Title |
C6/36 cells, Triptolide |
Sample type |
SRA |
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Source name |
C6/36 cells
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Organism |
Aedes albopictus |
Characteristics |
treatment: Triptolide protocol: Clontech/Nextera Non-stranded RNA-Seq
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Treatment protocol |
Aedes albopictus C6/36 cells were sub-cultured in a 24-well plate at a relatively low passage and set overnight to reach 70% confluency the day of treatment. Triptolide, Flavopiridol or DRB were added into the well, with final concentration of 5 uM, 0.5 uM and 30uM, respectively, in 0.1% DMSO. Cells were directly collected in Trizol for RNA extraction at 6 h post treatment.
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Growth protocol |
Aedes albopictusC6/36cells were obtained from ATCC[CRL-1660] and were cultured in Leibovitz’s L-15 medium supplemented with 10% fetal bovine serum (FBS), 0.02% L-glutamine, 100 U/ml of penicillin, 100 μg/ml of streptomycin, and 0.25 μg/ml of amphotericin B (Fungizone).
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Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted from cells using TRIzol (Invitrogen) and isopropanol precipitation according to the manufacturer’s instructions. After precipitation, the RNA pellet was washed twice with ice-cold freshly prepared 75% ethanol and subsequently air-dried and resuspended in water. RNA was quantified using Qubit RNA broad range kit. Full length cDNA generation was conducted on a Formulatrix Mantis liquid handling robot using Takara SMART-Seq v4 Ultra Low Input RNA kit. Then, sequencing libraries were created using the Illumina Nextera XT DNA Library Prep Kiton a SPT Labtech Mosquito liquid handling robot. Using these low-volume liquid handling robots, we were able to miniaturize reactions to 1/8. The resulting libraries were quantified, pooled and sequenced on an Illumina NextSeq 500 System using standard operating procedures.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
RSEM_TPM_table.csv
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Data processing |
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome AaloF1 with STAR aligner (version 2.7.3a ), using EnsGenembl 50 gene models. TPM values were generated using RSEM (version v1.3.0 ). Assembly: AaloF1 Supplementary files format and content: TPM gene expression in csv file for RNA-seq data.
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Submission date |
Jun 13, 2023 |
Last update date |
Jul 23, 2024 |
Contact name |
Shiyuan (Cynthia) Chen |
E-mail(s) |
shc@stowers.org
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Organization name |
Stowers Institute for Medical Research
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Department |
Computational Biology
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Street address |
1000 E 50th St
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City |
Kansas City |
State/province |
MO |
ZIP/Postal code |
64110 |
Country |
USA |
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Platform ID |
GPL22031 |
Series (1) |
GSE234878 |
Transcription inhibition in Aedes Albopictus C6/36 cells |
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Relations |
BioSample |
SAMN35725827 |
SRA |
SRX20672292 |
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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