|
| Status |
Public on Sep 22, 2021 |
| Title |
HCT116-J3-mock-RiboMethSeq |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
day: 3
|
| Treatment protocol |
Cells were mock-transfected or transfected with 40 nM of non-targeting siRNA, siCoilin #1 or siCoilin #2 and maintained for 1, 2 or 3 days before RNA extraction.
|
| Growth protocol |
Cell were maintained in DMEM + 10% heat-inactivated FBS, at 37°C with 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol
150 ng RNA was used to construct RiboMethSeq libraries using the procedure of Marchand et al. (PMID 27302133)
RiboMethSeq
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Adapter sequences were removed using Trimmomatic (0.36; LEADING:30 TRAILING:30 SLIDINGWINDOW:4:15 MINLEN:17 AVGQUAL:30). Only reads shorter than 90 nt were used for the analysis based on the length distribution of reads after adapter trimming.
Reads in the forward direction were mapped to an artificial genome containing ribosomal RNA sequences using bowtie2 (2.3.3.1; sensitive).
Mapped reads were analysed using the ‘R’ package ‘RNAmodR.RiboMethSeq’ and the Score C/RiboMethScore was used as a measurement for 2’-O methylation
Genome_build: hg19
Supplementary_files_format_and_content: .ends.csv: number of protected ends
Supplementary_files_format_and_content: .score.csv: scores per position
|
| |
|
| Submission date |
Jun 28, 2021 |
| Last update date |
Sep 22, 2021 |
| Contact name |
Tina M O'Grady |
| E-mail(s) |
[email protected]
|
| Phone |
504-988-1169
|
| Organization name |
Tulane Health Sciences Center
|
| Department |
Pathology
|
| Street address |
1430 Tulane Ave., SL79
|
| City |
New Orleans |
| State/province |
LA |
| ZIP/Postal code |
70112 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE156390 |
Role of TFIP11 in U6 snRNA modification and splicing efficiency |
| GSE179068 |
RiboMethSeq of HCT116 cells treated with siCoilin |
|
| Relations |
| BioSample |
SAMN19921077 |
| SRA |
SRX11245130 |
