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Status |
Public on Jan 02, 2023 |
Title |
Mettl3Inhibitor_actD_9h_rep1 |
Sample type |
SRA |
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Source name |
HEK293T
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Organism |
Homo sapiens |
Characteristics |
sample type: human cell line: HEK293T cell type: human embryonic kidney treatment: Mettl3 inhibitor STM2457 treatment (15h) and actD timepoints 9h, rep1
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Treatment protocol |
For combined treatment with Actinomycin D and m6A inhibitor STM2457 (DC Chemicals, Shanghai, #DC53045), the cells were seeded into 60-mm dishes and grown for one day until 50% confluent. Then, STM2457 (Yankova et al. 2021) compound was added at a final concentration of 5µM. After 6 hours of incubation, Actinomycin D was added (7.5µM) for the indicated time points and the cells were collected after a total treatment of 15 hours with STM2457.
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Growth protocol |
HEK293T cells were cultured in DMEM (Gibco) supplemented with 10% FBS and 1% Penicillin and Streptomycin.
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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 libraries were prepared from the full transcriptome.
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Library strategy |
RIP-Seq |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
HEK293T cells treated with Mettl3 inhibitor or untreated, and treated with actD for 0,3,6,9h. actD_Mettl3inh.bed
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Data processing |
Reads were mapped to hg19 genome annotation using STAR/2.7.9a (Dobin et al., 2013). Total read count per gene was computed with bedtools multicov (Quinlan and Hall 2010), with the samples ordered as non-treated 0 hours replicates, 3 hours replicates, 6 hours replicates, 9 hours replicates, followed by the treated samples ordered similarly. Assembly: hg19 Supplementary files format and content: Bed file with read quantification, ordered as non-treated 0 hours replicates, 3 hours replicates, 6 hours replicates, 9 hours replicates, followed by the treated samples ordered similarly.
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Submission date |
Sep 26, 2022 |
Last update date |
Jan 02, 2023 |
Contact name |
Anna Uzonyi |
E-mail(s) |
uzonyianna@gmail.com
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Organization name |
Weizmann Institute of Science
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Department |
Department of Molecular Genetics
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Lab |
Schraga Schwartz
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Street address |
234 Herzl street
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City |
Rehovot |
ZIP/Postal code |
7610001 |
Country |
Israel |
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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 |
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Relations |
BioSample |
SAMN31022822 |
SRA |
SRX17709826 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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