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Sample GSM4645461 Query DataSets for GSM4645461
Status Public on Nov 13, 2020
Title DLBCL derived cell line HT_1
Sample type SRA
 
Source name Cell line
Organism Homo sapiens
Characteristics sample type: DLBCL derived cell line
Extracted molecule total RNA
Extraction protocol Tissue and tumor samples were homogenized prior to RNA extraction, otherwise was whole cell RNA extracted using Trizol according to the manufacturer.
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 HT_1
whole cell RNA
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
Genome_build: RDNA reference sequence from Krogh et al, NAR 2016
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.
 
Submission date Jun 29, 2020
Last update date Nov 13, 2020
Contact name Nicolai Krogh
E-mail(s) nicolaikj@sund.ku.dk
Organization name University of Copenhagen
Department Department of Cellular and Molecular Medicine
Lab RNA Group - Prof. Henrik Nielsen
Street address Blegdamsvej 3B
City Copenhagen
ZIP/Postal code 2200
Country Denmark
 
Platform ID GPL17303
Series (1)
GSE153502 Profiling of ribose methylations in ribosomal RNA from diffuse large B-cell lymphoma patients for evaluation of ribosomes as drug targets
Relations
BioSample SAMN15399640
SRA SRX8633356

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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