 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 30, 2023 |
| Title |
HCT116_MeRIP |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: Colorectum
antibody: N6-Methyladenosine, 5′-monophosphate sodium salt (m6 A)
|
| 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 |
HCT116_m6A
|
| 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 |
SAMN36905553 |
| SRA |
SRX21310600 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7697986_HCT116_MeRIP.bw |
5.8 Mb |
(ftp)(http) |
BW |
| GSM7697986_HCT116_MeRIP_peaks.narrowPeak.gz |
194.8 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
