|
| Status |
Public on Jan 30, 2024 |
| Title |
GP4KO_3 (biol rep 3) |
| Sample type |
SRA |
| |
|
| Source name |
Flp-In T-Rex HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Flp-In T-Rex HEK293
genotype: GPATCH4 KO
|
| Growth protocol |
Wild-type (WT) and GPATCH4 knockout (GP4KO) HEK293 Flp-In T-Rex cells or HEK293 Flp-In T-Rex cells transfected with non-target siRNAs (siNT) or those targeting DHX15 (siDHX15) were grown at 37°C in 5% CO2 in high glucose DMEM supplemented with 10% foetal calf serum .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRI Reagent (Sigma-Aldrich) according to the manufacturer's instructions.
RiboMeth-seq: 5-10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5' phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
Trimmed reads
|
| Data processing |
Library strategy: RiboMeth-seq
Barcode separation using python script
Adaptor trimming using Cutadapt v. 2.0
Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1
Counting read ends and calculating RiboMeth-seq scores using python scripts
Assembly: Human rDNA reference sequence from Krogh et al, NAR 2016 and snRNA sequences from genome build hg38
Supplementary files format and content: MS Excel file contains 5' and 3' read count and calculated RiboMeth-seq score at all positions in the rRNA sequence.
Library strategy: RiboMeth-seq
|
| |
|
| Submission date |
Jun 27, 2023 |
| Last update date |
Jan 30, 2024 |
| Contact name |
Katherine Bohnsack |
| E-mail(s) |
[email protected]
|
| Organization name |
University Medical Centre Göttingen
|
| Street address |
Humboldtallee 23
|
| City |
Göttingen |
| ZIP/Postal code |
37073 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17303 |
| Series (2) |
| GSE230433 |
GPATCH4 regulates rRNA and snRNA 2'-O-methylation in both DHX15-dependent and -independent manners |
| GSE235949 |
GPATCH4 regulates rRNA and snRNA 2’-O-methylation in both DHX15-dependent and -independent manners [RiboMeth-seq] |
|
| Relations |
| BioSample |
SAMN36002422 |
| SRA |
SRX20795222 |
