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| Status |
Public on May 17, 2023 |
| Title |
E14-Mettl3-KO paused, time 0, rep2 |
| Sample type |
SRA |
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| Source name |
E14
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| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic stem cells
cell line: E14
genotype: Mettl3-KO
treatment: paused
time: 0h
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| Treatment protocol |
Cells were pre-incubated with 100μM S4U, protected from light and with media exchange every 3h, for a total of 12h. Then, the medium was changed back to standard (no S4U), and cells were collected at different times (0h, 1h, 3h, 8h).
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| Growth protocol |
ES cells were grown on gelatin for 2 weeks in FBS/LIF media, under paused condition (200 nM INK128).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from equal number of ESCs (5x10^5 cells),RNA extraction using phenol-chloroform extraction, as per manufacturer’s instructions. RNAs were treated with 10mM iodoacetamide and ethanol precipitated.
Library preparation was done with Quant-seq 3′-end mRNA library preparation (Lexogen) using 100ng RNA.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
KO_0.2
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| Data processing |
Libraries were trimmed of adaptors and quality-checked using Trim Galore! v0.4.0, and then aligned to the mm10 transcriptome with ERCC sequences using TopHat2115 v2.0.13. Gene counts were obtained from the featureCounts function of subread (v1.5.0) with options: -t exon -g gene_id.
3UTR raw counts were imported into R and analyzed with edgeR (v3.32.1). Conversions counts were normalized to total counts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts (total and T-to-C conversion) of all genes for all samples.
Supplementary files format and content: tab-delimited text file with expression levels (log2) for all samples with normalization; and half-lives of all transcripts in paused condition calculated for WT and KO ESCs separately.
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| Submission date |
Apr 02, 2023 |
| Last update date |
May 17, 2023 |
| Contact name |
Evelyne Anne Collignon |
| Organization name |
Lunenfeld-Tanenbaum Research Institute
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| Lab |
Ramalho-Santos lab
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| Street address |
60 Murray Street, Box42,
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| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5T 3L9 |
| Country |
Canada |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE202848 |
m6A RNA methylation orchestrates transcriptional dormancy during paused pluripotency |
| GSE228734 |
m6A RNA methylation orchestrates transcriptional dormancy during paused pluripotency [SLAM-seq] |
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| Relations |
| BioSample |
SAMN34041282 |
| SRA |
SRX19844921 |
| 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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