|
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 |