|
| Status |
Public on Jan 02, 2023 |
| Title |
input_rep1_WTdeg_4h |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: human
cell line: HEK293T
cell type: human embryonic kidney
treatment: DMSO, 4h
|
| Treatment protocol |
In 6 well plate, cells were cultivated at 70% confluency and treated with DMSO 1:1000 or 50 nM dTAG13 (Sigma-Aldrich) in DMSO, and harvested after 4, 8, 16 and 24 hours post-treatment.
|
| Growth protocol |
HEK293T and HEK293T Y14-HA-dTAG cells were maintained in DMEM high glucose (Dutscher) supplemented with 10% of fetal bovine serum (Sigma-Aldrich), and 1% of penicillin and streptomycin (Sigma-Aldrich).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted with BIO TRI RNA reagent (Bio-lab)
RNA was poly-A selected with oligo dT-beads (Dynabeads® mRNA DIRECT™ Kit life tech) and subjected to m6Aseq2 according to Dierks et al, 2021 Nature Methods.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The reads were aligned with STAR/2.7.9a to the hg19 genome. For further analysis, the bam files were filtered for uniquely aligned reads and processed by the bam2Endreads Rscript (Garcia-Campos et al. 2019) for RNA fragment coverage in transcript space.
Assembly: hg19
Supplementary files format and content: Rdata files output of the bam2ReadEnds script of txtools.
|
| |
|
| Submission date |
Sep 26, 2022 |
| Last update date |
Jan 02, 2023 |
| Contact name |
Anna Uzonyi |
| E-mail(s) |
uzonyianna@gmail.com
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Department of Molecular Genetics
|
| Lab |
Schraga Schwartz
|
| Street address |
234 Herzl street
|
| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE204980 |
Exclusion of m6A from splice-site-proximal regions by the exon-junction complex dictates m6A topologies and mRNA stability |
|
| Relations |
| BioSample |
SAMN31022760 |
| SRA |
SRX17709816 |
