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Sample GSM7135735 Query DataSets for GSM7135735
Status Public on May 17, 2023
Title E14-WT paused, time 8h, rep2
Sample type SRA
 
Source name E14
Organism Mus musculus
Characteristics cell type: embryonic stem cells
cell line: E14
genotype: WT
treatment: paused
time: 8h
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).
Growth protocol ES cells were grown on gelatin for 2 weeks in FBS/LIF media, under paused condition (200 nM INK128).
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description WT_8.2
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.
 
Submission date Apr 02, 2023
Last update date May 17, 2023
Contact name Evelyne Anne Collignon
Organization name Lunenfeld-Tanenbaum Research Institute
Lab Ramalho-Santos lab
Street address 60 Murray Street, Box42,
City Toronto
State/province ON
ZIP/Postal code M5T 3L9
Country Canada
 
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]
Relations
BioSample SAMN34041273
SRA SRX19844930

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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