|
| Status |
Public on Mar 08, 2023 |
| Title |
KO1 IP |
| Sample type |
SRA |
| |
|
| Source name |
ALKBH5flox/flox, αMyHC-Cre-DOX-1
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Heart
rip antibody: Anti-m6A (Synaptic Systems, Cat. No 202 003)
genotype: ALKBH5flox/flox, {alpha}MyHC-Cre-DOX-1
treatment: Doxorubicin
|
| Treatment protocol |
Mice were intraperitoneally injected with 20mg/kg doxorubicin.
|
| Growth protocol |
Myocardial tissues of ALKBH5-Control(WT, ALKBH5flox/flox) mice and ALKBH5 myocardial-specific knockout(KO, ALKBH5flox/flox, αMyHC-Cre) mice were methylated RNA immunoprecipitation sequencing (MeRIP-seq) and MeRIP-seq-qPCR
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Oiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and MeRIP-seq-qPCR
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequencellow-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm 10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction:
Read count extraction and normalization were performed using CC genomic benchwork
Assembly: GRCm38.p6
Supplementary files format and content: bigwig files for each samples
|
| |
|
| Submission date |
Feb 01, 2023 |
| Last update date |
Mar 08, 2023 |
| Contact name |
Rifeng Gao |
| E-mail(s) |
grfvictory@zju.edu.cn
|
| Organization name |
Zhejiang University
|
| Street address |
No. 88 Jiefang Road
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310009 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE224215 |
m6A Demethylase ALKBH5 attenuates doxorubicin-induced cardiotoxicity via posttranscriptional stabilization of Rasal3 |
|
| Relations |
| BioSample |
SAMN33005029 |
| SRA |
SRX19243971 |
