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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 01, 2023 |
| Title |
mES_Nanopore_dRNAseq_WT |
| Sample type |
SRA |
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| Source name |
mouse 129 embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: mESC
sample type: WT cellular mRNA
sequence type: Nanopore direct RNA sequencing
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| Growth protocol |
Wild type (WT) of mouse 129 embryonic stem cells (mESCs) and Mettl3 knockout (KO) mESCs were provided by Dr. Jiekai Chen (Guangzhou Institutes of Biomedicine and Health, CAS).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific, 15596026) and the mRNA was purified using Dynabeads mRNA Purification Kit (Thermo Fisher Scientific, 61006). mRNA was treated by TURBO DNase (Thermo Fisher, AM2238) at 37 ℃ for 30 min and purified by ethanol precipitation or RNA Clean & Concentrator-5 kit (Zymo Research, R1015) to remove genomic DNA.
Nanopore direct RNA sequencing libraries were prepared using about 800ng ployA RNA following the SQK-RNA002 kit protocol (version: DRS_9080_v2_revK_14Aug2019). RNA Sequencing on the MinION platform was performed on the FLO-MIN106 flow cell, and raw data was generated by MinKNOW (v20.06.9).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
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| Data processing |
After default live basecalling in MinKNOW (v20.06.9), reads that passed the quality threshold (7) were base-called again with newer versions of Guppy (v5.0.7) with default parameters. Reads that passes the quality threshold (7) for the second time were kept. Then m6A sites detected by 10 ONT tools (Tombo (v1.5.1), MINES, Nanom6A (v2.0), m6Anet (v1.0), Nanocompore (v1.0.0), Xpore (v2.0), DiffErr (v0.2), DRUMMER, ELIGOS (v2.0.1) and Epinano (v1.2.0)) with their respective default parameters but limited in the RRACH motif.
Genome_build: mm10 (mouse)
Supplementary_files_format_and_content: bed; m6A sites detected by 10 ONT tools.
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| Submission date |
Jan 28, 2022 |
| Last update date |
Mar 03, 2023 |
| Contact name |
Zhendong Zhong |
| E-mail(s) |
zhongzhd@mail2.sysu.edu.cn
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| Phone |
19806835958
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| Organization name |
Sun Yat-sen University
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| Department |
School of Life Sciences
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| Street address |
Xingangxi Roda 135#
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510275 |
| Country |
China |
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| Platform ID |
GPL24973 |
| Series (1) |
| GSE195618 |
Systematic comparison of tools used for m6A mapping from nanopore direct RNA sequencing |
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| Relations |
| BioSample |
SAMN25352406 |
| SRA |
SRX13965943 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5841801_mES_WT.m6A_ELIGOS.bed.gz |
81.1 Kb |
(ftp)(http) |
BED |
| GSM5841801_mES_WT.m6A_Epinano.bed.gz |
573.7 Kb |
(ftp)(http) |
BED |
| GSM5841801_mES_WT.m6A_MINES.bed.gz |
194.3 Kb |
(ftp)(http) |
BED |
| GSM5841801_mES_WT.m6A_Nanom6A.bed.gz |
228.3 Kb |
(ftp)(http) |
BED |
| GSM5841801_mES_WT.m6A_Tombo.bed.gz |
938.6 Kb |
(ftp)(http) |
BED |
| GSM5841801_mES_WT.m6A_Xpore.bed.gz |
74.1 Kb |
(ftp)(http) |
BED |
| GSM5841801_mES_WT.m6A_m6Anet.bed.gz |
279.4 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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