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Sample GSM6499557 Query DataSets for GSM6499557
Status Public on Aug 01, 2024
Title mouse intestine MODEK cells, control,rep3 [IRcon3]
Sample type SRA
 
Source name MODEK cells
Organism Mus musculus
Characteristics cell line: MODEK cells
cell type: small intestine epithelium
genotype: Wild Type
treatment: no treatment
Treatment protocol The cell was irradiated with 0, 4 and 12 Gy at 25°C with a dose rate of 87 cGy/min using a 60Co gamma-ray source. Each radiation dose included three parallel experimental groups, and cell pellets were collected at 0 h, 24 h and 48 h.
Growth protocol Mouse intestinal epithelial cells MODE-K was cultured in Dulbecco's modified Eagle's medium containing 10% fetal bovine serum, 100 U/ml penicillin and 100 µg/ml streptomycin at 37°C in T25 cell culture flasks.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model PromethION
 
Description MODEK cells, control group, rep3
Data processing A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. 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). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Supplementary files format and content: tab-delimited text files include FPKM values
 
Submission date Aug 21, 2022
Last update date Aug 01, 2024
Contact name Changhui Ge
E-mail(s) chge502@163.com, chge88@sina.com
Organization name Beijing institute of Radiation Medicine
Department Department of Experimental Hematology and Biochemistry
Street address 27 Taiping Rd., Haidian Dist.
City Beijing
ZIP/Postal code 100850
Country China
 
Platform ID GPL26624
Series (1)
GSE211709 Regulation of pyroptosis in radiation induces mouse intestine cells
Relations
BioSample SAMN30429689
SRA SRX17163194

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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