GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE99970 Query DataSets for GSE99970
Status Public on Sep 23, 2017
Title Thiol-linked alkylation for the metabolic sequencing of RNA [SLAM-seq pulse/chase labeling in wildtype mES cells]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Gene expression profiling by high-throughput sequencing reveals qualitative and quantitative changes in RNA species at steady-state but obscures the intracellular dynamics of RNA transcription, processing and decay. We developed thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq), an orthogonal chemistry-based epitranscriptomics-sequencing technology that uncovers 4-thiouridine (s4U)-incorporation in RNA species at single-nucleotide resolution. In combination with well-established metabolic RNA labeling protocols and coupled to standard, low-input, high-throughput RNA sequencing methods, SLAM-seq enables rapid access to RNA polymerase II-dependent gene expression dynamics in the context of total RNA. When applied to mouse embryonic stem cells, SLAM-seq provides global and transcript-specific insights into pluripotency-associated gene expression. We validated the method by showing that the RNA-polymerase II-dependent transcriptional output scales with Oct4/Sox2/Nanog-defined enhancer activity; and provides quantitative and mechanistic evidence for transcript-specific RNA turnover mediated by post-transcriptional gene regulatory pathways initiated by microRNAs and N6-methyladenosine. SLAM-seq facilitates the dissection of fundamental mechanisms that control gene expression in an accessible, cost-effective, and scalable manner.
Overall design Wildtype mouse embryonic stem cells (mES cells) were subjected to s4U metabolic RNA labeling for 24 h (pulse, 100 µM s4U), followed by washout (chase) using non-thiol-containing uridine. Total RNA was prepared at various time points along the chase (0h, 0.5h, 1h, 3h, 6h, 12h, and 24h). Total RNA was then subjected to alkylation and mRNA 3ʹ end sequencing library preparation (QuantSeq, Lexogen).
Contributor(s) Herzog VA, Reichholf B, Neumann T, Rescheneder P, Bhat P, Burkard TR, Wlotzka W, von Haeseler A, Zuber J, Ameres SL
Citation(s) 28945705, 31109287
Submission date Jun 13, 2017
Last update date Jul 25, 2021
Contact name Brian Reichholf
Organization name IMBA
Lab Stefan Ameres
Street address Doktor-Bohr-Gasse 3
City Vienna
ZIP/Postal code 1030
Country Austria
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (27)
GSM2666816 34330 mESC no s4U Rep 1
GSM2666817 34343 mESC no s4U Rep 2
GSM2666818 34356 mESC no s4U Rep 3
This SubSeries is part of SuperSeries:
GSE99978 Thiol-linked alkylation for the metabolic sequencing of RNA
BioProject PRJNA390468
SRA SRP109169

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE99970_GSE99970_mESC_UTR_regions.bed.gz 352.7 Kb (ftp)(http) BED
GSE99970_GSE99970_mESC_counting_windows.bed.gz 339.2 Kb (ftp)(http) BED
GSE99970_RAW.tar 19.2 Mb (http)(custom) TAR (of TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap