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Sample GSM7512286 Query DataSets for GSM7512286
Status Public on Jan 30, 2024
Title siNT_2 (biol rep 2)
Sample type SRA
 
Source name Flp-In T-Rex HEK293
Organism Homo sapiens
Characteristics cell line: Flp-In T-Rex HEK293
genotype: WT, siNon-Target
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) katherine.bohnsack@med.uni-goettingen.de
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 SAMN36002420
SRA SRX20795224

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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