U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX18700348: GSM6833206: 13-NBS; Homo sapiens; Bisulfite-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 5M spots, 1G bases, 290.6Mb downloads

External Id: GSM6833206_r1
Submitted by: CIBIO, University of Trento
Study: Alterations of ribosomal RNA pseudouridylation in human breast cancer
show Abstracthide Abstract
RNA modifications are key regulatory factors for several biological and pathological processes. They are abundantly represented on ribosomal RNA (rRNA), where they contribute to regulate ribosomal function in mRNA translation. Altered RNA modification pathways have been linked to tumorigenesis as well as to other human diseases. In this study we quantitatively evaluated the site-specific pseudouridylation pattern in rRNA in breast cancer samples exploiting the RBS-Seq technique involving RNA bisulfite treatment coupled with a new NGS approach. We found a wide variability among patients at different sites. The most dysregulated positions in tumors turned out to be hypermodified with respect to a reference RNA. As for 2'O-methylation level of rRNA modification, we detected variable and stable pseudouridine sites, with the most stable sites being the most evolutionary conserved. We also observed that pseudouridylation levels at specific sites are related to some clinical and bio-pathological tumor features and are able to distinguish different patient clusters. This study is the first example of the contribution that newly available high-throughput approaches for site specific pseudouridine detection can provide to the understanding of the intrinsic ribosomal changes occurring in human tumors. Overall design: RBS-seq of 77 bisulfite-treated and untreated breast cancer samples and 5 reference samples
Sample: 13-NBS
SAMN32231931 • SRS16141448 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: GSM6833206
Instrument: Illumina NovaSeq 6000
Strategy: Bisulfite-Seq
Source: TRANSCRIPTOMIC
Selection: RANDOM
Layout: PAIRED
Construction protocol: Total RNA was extracted from frozen specimens of 34 breast tumors using the mirVana miRNA isolation kit (ThermoFisher Scientific). Human total RNA (Human XpressRef Universal Total RNA, Qiagen) was used as normal reference samples for analysis. RNA library construction was performed with the TruSeq Stranded mRNA kit (Illumina) with some modifications. In particular, 100 ng of each beads-purified aqueous RNA samples were submitted to a second round of RNACleanXP beads purification to substitute water with the FPF (Fragment, Prime, Finish Mix) solution included in the library kit. Then the manufacturer's protocol was followed. The Unique-dual indexes (Illumina) were used in the adapters ligation step. Each individual library was then quantified and quality-controlled using Qubit Fluorometer (ThermoFisher Scientific) and LabChip GX (Perkin Elmer). An unbalanced pooling design was used to achieve a ratio of 1 to 8 between untreated and BS-treated samples. After libraries unbalanced pooling, the final pool was quality checked again with Qubit, LabChip GX, and qPCR (KAPA and BIORAD).
Runs: 1 run, 5M spots, 1G bases, 290.6Mb
Run# of Spots# of BasesSizePublished
SRR227389704,977,5731G290.6Mb2023-06-07

ID:
25765655

Supplemental Content

Search details

See more...

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...