|
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 |