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Sample GSM7476146 Query DataSets for GSM7476146
Status Public on Jul 23, 2024
Title C6/36 cells, Triptolide
Sample type SRA
 
Source name C6/36 cells
Organism Aedes albopictus
Characteristics treatment: Triptolide
protocol: Clontech/Nextera Non-stranded RNA-Seq
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.
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).
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description RSEM_TPM_table.csv
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.
 
Submission date Jun 13, 2023
Last update date Jul 23, 2024
Contact name Shiyuan (Cynthia) Chen
E-mail(s) shc@stowers.org
Organization name Stowers Institute for Medical Research
Department Computational Biology
Street address 1000 E 50th St
City Kansas City
State/province MO
ZIP/Postal code 64110
Country USA
 
Platform ID GPL22031
Series (1)
GSE234878 Transcription inhibition in Aedes Albopictus C6/36 cells
Relations
BioSample SAMN35725827
SRA SRX20672292

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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