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| Status |
Public on Nov 03, 2022 |
| Title |
A6 IP APP/PS1 AD mice , m6A RNA |
| Sample type |
SRA |
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| Source name |
cortex, hippocampus and cerebellum
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| Organism |
Mus musculus |
| Characteristics |
tissue: frozen mouse brain
tissue: cortex, hippocampus and cerebellum
cell type: nerve cell
age: 9-month-old
genotype: APP/PS1 AD mice
treatment: m6A RNA
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| Extracted molecule |
total RNA |
| Extraction protocol |
m6A RNA-Seq service was provided by Cloudseq Biotech Inc. (Shanghai, China). Briefly, m6A RNA immunoprecipitation was performed with the GenSeqTM m6A RNA IP Kit (GenSeq Inc., China) by following the manufacturer's instructions.
Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
both the input samples without immunoprecipitation and the m6A IP samples were submitted to 150-bp paired-end sequencing
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| Data processing |
library strategy:circRNA-seq
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
First, clean reads of input libraries were aligned to reference genome (UCSC MM10) by STAR software.
Reverse transcription (RT)-qPCR was used to evaluate eight genes with differentially methylated sites according to circRNA m6A-seq
Then circRNAs were identified by DCC software using the STAR alignment results
After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps
These peaks identified by both softwares overlapping with exons of mRNA, LncRNA and circRNA were figured out and choosed by home-made scripts
GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes, the associated genes of differentially methylated LncRNAs and the source genes of differentially methylated circRNAs separately.
Assembly: MM10
Supplementary files format and content: xlsx files BED files
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| Submission date |
Oct 31, 2022 |
| Last update date |
Nov 03, 2022 |
| Contact name |
song han |
| E-mail(s) |
h1558854@126.com
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| Phone |
+8615588545086
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| Organization name |
The Second Hospital of Shandong University， Cheeloo College of Medicine，Shandong University
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| Street address |
Tianqiao District
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| City |
Jinan City |
| State/province |
ShanDong province |
| ZIP/Postal code |
250000 |
| Country |
China |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE216901 |
Differential Methylation of CircRNA m6A in the APP/PS1 Alzheimer's Disease Mouse Model [cirRNA-seq] |
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| Relations |
| BioSample |
SAMN31530622 |
| SRA |
SRX18086126 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6697377_A6.LncRNA.m6A.bed.gz |
35.4 Kb |
(ftp)(http) |
BED |
| GSM6697377_A6.circRNA.m6A.bed.gz |
72.7 Kb |
(ftp)(http) |
BED |
| GSM6697377_A6.mRNA.m6A.bed.gz |
53.4 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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