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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 07, 2024 |
| Title |
Single cell discovery of m6A RNA modifications in the hippocampus |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
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| Summary |
N6-methyladenosine (m6A) is a prevalent and highly regulated RNA modification essential for RNA metabolism and normal brain function. It is particularly important in the hippocampus, where m6A is implicated in neurogenesis and learning. Although extensively studied, its presence and impact in specific cell types remain poorly understood. We investigated m6A in the hippocampus at the single-cell level, revealing a comprehensive landscape of m6A modifications within individual cells.
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| Overall design |
We identified m6A RNA sites in bulk RNA sequencing and in single cell data by detecting RNA editing sites that were introduced near m6A sites. We first tested our approach in HEK293T cells, with bulk RNA-seq. We transfected our samples with YTH viruses that caused editing near m6A sites, while YTHmut viruses and APOBEC1 and wild type samples were used as background controls. After we verified this approach in HEK293T cells, we applied it the mouse hippocampus also with bulk RNA-seq. We then performed single cell sequencing to identify m6A sites in single cells by identifying mutations in the sequencing data. We confirmed our data with m6A-RNA immunoprecipitation and sequencing (m6A-RIP seq).
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| Web link |
https://dnalaboratory.org
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| Contributor(s) |
Feng S, Tallaetxe-Abete M, Zhang Y, Peng Y, Zhou H, Dong M, Larrea E, Xue L, Zhang L, Koziol MJ |
| Citation(s) |
39009472 |
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| Submission date |
Aug 15, 2023 |
| Last update date |
Aug 06, 2024 |
| Contact name |
Magdalena Justyna Koziol |
| E-mail(s) |
mjk@cibr.ac.cn
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| Organization name |
Chinese Institute for Brain Researach, CIBR
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| Street address |
Science Park Road
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| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
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| Platforms (2) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (43)
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| GSM7710934 |
Hippocampus, m6A RIP-pulldown, rep2 |
| GSM7710935 |
Hippocampus, m6A RIP-input, rep3 |
| GSM7710936 |
Hippocampus, m6A RIP-pulldown, rep3 |
| GSM7710937 |
Bulk, HEK293T, APOBEC1-E, rep1 |
| GSM7710938 |
Bulk, HEK293T, APOBEC1-E, rep2 |
| GSM7710939 |
Bulk, HEK293T, APOBEC1-E, rep3 |
| GSM7710940 |
Bulk, HEK293T, E-APOBEC1, rep1 |
| GSM7710941 |
Bulk, HEK293T, E-APOBEC1, rep2 |
| GSM7710942 |
Bulk, HEK293T, E-APOBEC1, rep3 |
| GSM7710943 |
Bulk, HEK293T, E-Mut, rep1 |
| GSM7710944 |
Bulk, HEK293T, E-Mut, rep2 |
| GSM7710945 |
Bulk, HEK293T, E-Mut, rep3 |
| GSM7710946 |
Bulk, HEK293T, E-YTH, rep1 |
| GSM7710947 |
Bulk, HEK293T, E-YTH, rep2 |
| GSM7710948 |
Bulk, HEK293T, E-YTH, rep3 |
| GSM7710949 |
Bulk, HEK293T, Mock, rep1 |
| GSM7710950 |
Bulk, HEK293T, Mock, rep2 |
| GSM7710951 |
Bulk, HEK293T, Mock, rep3 |
| GSM7710952 |
Bulk, HEK293T, Mut-E, rep1 |
| GSM7710953 |
Bulk, HEK293T, Mut-E, rep2 |
| GSM7710954 |
Bulk, HEK293T, Mut-E, rep3 |
| GSM7710955 |
Bulk, HEK293T, YTH-E, rep1 |
| GSM7710956 |
Bulk, HEK293T, YTH-E, rep2 |
| GSM7710957 |
Bulk, HEK293T, YTH-E, rep3 |
| GSM7710958 |
Bulk, Hippocampus, E-APOBEC1, rep1 |
| GSM7710959 |
Bulk, Hippocampus, E-APOBEC1, rep2 |
| GSM7710960 |
Bulk, Hippocampus, E-APOBEC1, rep3 |
| GSM7710961 |
Bulk, Hippocampus, E-Mut, rep1 |
| GSM7710962 |
Bulk, Hippocampus, E-Mut, rep2 |
| GSM7710963 |
Bulk, Hippocampus, E-Mut, rep3 |
| GSM7710964 |
Bulk, Hippocampus, E-YTH, rep1 |
| GSM7710965 |
Bulk, Hippocampus, E-YTH, rep2 |
| GSM7710966 |
Bulk, Hippocampus, E-YTH, rep3 |
| GSM7710967 |
Bulk, Hippocampus, Wildtype, rep1 |
| GSM7710968 |
Bulk, Hippocampus, Wildtype, rep2 |
| GSM7710969 |
Bulk, Hippocampus, Wildtype, rep3 |
| GSM7710970 |
Single cell, Hippocampus, E-YTH |
| GSM7710971 |
Single cell, Hippocampus, E-Mut |
| GSM8254991 |
Single cell, Hippocampus, Metll3CKOE-YTH |
| GSM8254992 |
Single cell, Hippocampus, Metll3CKOE-Mut |
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| Relations |
| BioProject |
PRJNA1005593 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE240863_01-WT_rep1_summits.bed.gz |
134.5 Kb |
(ftp)(http) |
BED |
| GSE240863_02_WT_rep2_summits.bed.gz |
134.4 Kb |
(ftp)(http) |
BED |
| GSE240863_03-WT_rep3_summits.bed.gz |
144.6 Kb |
(ftp)(http) |
BED |
| GSE240863_RAW.tar |
626.6 Mb |
(http)(custom) |
TAR (of CSV, RDS, TXT) |
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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