|
| Status |
Public on Apr 13, 2022 |
| Title |
si-ALKBH5 rep 2 Input |
| Sample type |
SRA |
| |
|
| Source name |
oral squamous cell carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Cal27
antibody: none
transfection: siALKBH5
|
| Treatment protocol |
cells were transfected with ALKBH5-specific siRNA using RNAiMax reagent.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
m6A RNA immunoprecipitation was performed with the GenSeq™ 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).
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
First, clean reads of all libraries were aligned to the reference genome (HG19) 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 were figured out and choosed by home-made scripts.
Genome_build: HG19
Supplementary_files_format_and_content: Matrix table with peaks calling results for every peak and every sample
|
| |
|
| Submission date |
Oct 13, 2021 |
| Last update date |
Apr 13, 2022 |
| Contact name |
Hailong Ma |
| E-mail(s) |
mahl21@sjtu.edu.cn
|
| Organization name |
Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine
|
| Street address |
Zhizaoju Rd
|
| City |
Shanghai |
| ZIP/Postal code |
200011 |
| Country |
China |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE185885 |
ALKBH5 promotes tumor progression by decreasing RIG-I expression mediated by N6-methyladenosine-dependent HNRNPC binding in HNSCC [MeRIP-seq] |
| GSE185888 |
ALKBH5 promotes tumor progression by decreasing RIG-I expression mediated by N6-methyladenosine-dependent HNRNPC binding in HNSCC |
|
| Relations |
| BioSample |
SAMN22252655 |
| SRA |
SRX12601767 |
