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Series GSE133361 Query DataSets for GSE133361
Status Public on Sep 09, 2020
Title Determination of isoform-specific RNA structure with nanopore long reads
Organisms Bacillus subtilis; Saccharomyces cerevisiae; Tetrahymena thermophila; Homo sapiens; Dengue virus; Oceanobacillus iheyensis
Experiment type Other
Summary Current methods for determening RNA structure with short-read sequencing cannot capture most differences between distinct transcript isoforms. Here, we present RNA structure analysis using nanopore sequencing (PORE-cupine),which combines structure probing using chemical modifications with direct long-read RNA sequencing and machine learning to detect secondary structures in cellular RNAs. PORE-cupine also captures global structural features, such as RNA binding protein (RBP) binding sites and reactivity differences at single nucleotide variants (SNVs). We show that shared sequences in different transcript isoforms of the same gene can fold into different structures, highlighting the importance of long-read sequencing for obtaining phase information. We also demonstrate that structural differences between transcript isoforms of the same gene lead to differences in translation efficiency. By revealing isoform-specific RNA structure, PORE-cupine will deepen our understanding of the role of structures in controlling gene regulation.
Overall design 90 libraries in total
The libraries consist of two types of samples, unmodified control and modified libraries.
Training libraries were used to train the models.
Test libraries were used to evaluate the parameters obtained from training.
TPP libraries were used to determine structural changes between samples incubated with and without its ligand.
H9 libraries were used to study structural changes in the human transcriptome.
Two replicates of H9 were sequenced with Illumnia sequencing.
Contributor(s) Aw JG, Lim SW, Wang JX
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Submission date Jun 26, 2019
Last update date Apr 22, 2021
Contact name Aw Jong Ghut Ashley
Organization name Genome Institute of Singapore
Street address 60 Biopolis St
City singapore
ZIP/Postal code 138672
Country Singapore
Platforms (5)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL24106 MinION (Homo sapiens)
GPL26846 MinION (Tetrahymena thermophila)
Samples (21)
GSM3906238 H9_unmodifed
GSM3906239 H9_treated_bio_1
GSM3906240 H9_treated_bio_2
BioProject PRJNA551261
SRA SRP213925

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE133361_H9_lnc_1.csv.gz 3.4 Mb (ftp)(http) CSV
GSE133361_H9_lnc_2.csv.gz 4.7 Mb (ftp)(http) CSV
GSE133361_H9_mRNA_1.csv.gz 114.3 Mb (ftp)(http) CSV
GSE133361_H9_mRNA_2.csv.gz 146.1 Mb (ftp)(http) CSV
GSE133361_Output_16s_bsub_1.csv.gz 27.0 Kb (ftp)(http) CSV
GSE133361_Output_16s_bsub_2.csv.gz 29.0 Kb (ftp)(http) CSV
GSE133361_Output_B.sub_TPP_li_250_1.csv.gz 7.0 Kb (ftp)(http) CSV
GSE133361_Output_B.sub_TPP_li_250_2.csv.gz 5.3 Kb (ftp)(http) CSV
GSE133361_Output_B.sub_TPP_li_750_1.csv.gz 7.1 Kb (ftp)(http) CSV
GSE133361_Output_B.sub_TPP_li_750_2.csv.gz 4.7 Kb (ftp)(http) CSV
GSE133361_Output_B.sub_TPPli_1.csv.gz 6.0 Kb (ftp)(http) CSV
GSE133361_Output_B.sub_TPPli_2.csv.gz 6.1 Kb (ftp)(http) CSV
GSE133361_Output_B.sub_TPPli_3.csv.gz 7.1 Kb (ftp)(http) CSV
GSE133361_Output_B.sub_TPPno_li_1.csv.gz 5.4 Kb (ftp)(http) CSV
GSE133361_Output_B.sub_TPPno_li_2.csv.gz 5.8 Kb (ftp)(http) CSV
GSE133361_Output_B.sub_TPPno_li_3.csv.gz 7.0 Kb (ftp)(http) CSV
GSE133361_Output_Lysine_riboswitch_1.csv.gz 6.4 Kb (ftp)(http) CSV
GSE133361_Output_Lysine_riboswitch_2.csv.gz 6.4 Kb (ftp)(http) CSV
GSE133361_Output_RSP29_1.csv.gz 6.2 Kb (ftp)(http) CSV
GSE133361_Output_RSP29_2.csv.gz 6.0 Kb (ftp)(http) CSV
GSE133361_Output_adocbl_1.csv.gz 7.1 Kb (ftp)(http) CSV
GSE133361_Output_adocbl_2.csv.gz 7.0 Kb (ftp)(http) CSV
GSE133361_Output_lnc_1.csv.gz 955.7 Kb (ftp)(http) CSV
GSE133361_Output_lnc_2.csv.gz 1.3 Mb (ftp)(http) CSV
GSE133361_Output_mRNA_1.csv.gz 54.4 Mb (ftp)(http) CSV
GSE133361_Output_mRNA_2.csv.gz 88.0 Mb (ftp)(http) CSV
GSE133361_Output_ncRNA_1.csv.gz 54.4 Mb (ftp)(http) CSV
GSE133361_Output_ncRNA_2.csv.gz 88.0 Mb (ftp)(http) CSV
GSE133361_Output_tetra_1x_1.csv.gz 7.7 Kb (ftp)(http) CSV
GSE133361_Output_tetra_1x_2.csv.gz 8.2 Kb (ftp)(http) CSV
GSE133361_Output_tetra_denatured.csv.gz 7.9 Kb (ftp)(http) CSV
GSE133361_Output_tetra_unmod.csv.gz 7.8 Kb (ftp)(http) CSV
GSE133361_RAW.tar 16.6 Gb (http)(custom) TAR (of TAR)
GSE133361_integrated_point_mutations.txt.gz 456.8 Kb (ftp)(http) TXT
GSE133361_sample-csv-relations.xlsx 14.1 Kb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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