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| Status |
Public on Jan 02, 2023 |
| Title |
control_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: non-treated samples related to the Mettl3 inhibitor STM2457 treatment (15h), actD treatment 9h, rep1
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| Treatment protocol |
For treatment with Actinomycin D the cells were seeded into 60-mm dishes and grown for one day until 50% confluent. Actinomycin D was added (7.5µM) for the indicated time points.
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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 |
SAMN31022778 |
| SRA |
SRX17709798 |
| 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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