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Sample GSM7697994 Query DataSets for GSM7697994
Status Public on Dec 30, 2023
Title COLO320DM_INPUT
Sample type SRA
 
Source name COLO320DM
Organism Homo sapiens
Characteristics cell line: COLO320DM
cell type: Colon
Growth protocol DMEM, 10% fetal bovine serum, 1X pencillin/streptomycin. Cells were cultured at 37°C at 5% CO2
Extracted molecule total RNA
Extraction protocol 300µg of total RNA was extracted from the cell lines using Trizol and Nucleospin RNA extraction kit(macherey nagel-GMBH)
Approximately 300µg of total RNA was initially used for the fragmentation process to achieve the fragment length of ~100 nucleotides. The fragmented RNA was further enriched using Magna MeRIP™ m6A Kit- Transcriptome-wide Profiling kit (Cat. no: 17-10499, Sigma-Aldrich, USA) according to the manufacturer’s instructions to get m6A enriched RNA. About 10% of the fragmented RNA was saved as Input control.
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description COLO320DM_RNAseq
Data processing library strategy: meRIP-seq
The raw reads were processed using cutadapt for trimming the adapter sequences and the sequence quality was checked with FASTQC.
The reads were aligned with human reference genome hg19 using bwa-mem algorithm.
MACS2 peak calling was performed with a p-value of 0.05 to obtain the peaks from the colon cancer cell line samples.
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak
 
Submission date Aug 09, 2023
Last update date Dec 30, 2023
Contact name Samson Mani
E-mail(s) samsonn.m@gmail.com
Phone 6381741841
Organization name Cancer Institute (WIA)
Department Molecular Oncology
Street address 38, Sardar Patel Road
City Chennai
State/province Tamilnadu
ZIP/Postal code 600036
Country India
 
Platform ID GPL24676
Series (1)
GSE240438 Epitranscriptome profiling of m6A in colon cancer cell lines
Relations
BioSample SAMN36905545
SRA SRX21310603

Supplementary file Size Download File type/resource
GSM7697994_COLO320DM_INPUT.bw 9.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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