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Series GSE60988 Query DataSets for GSE60988
Status Public on Sep 03, 2015
Title Tracking distinct RNA populations using efficient and reversible covalent chemistry
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary We describe a chemical method to label and purify 4-thiouridine (s4U) -containing RNA. We demonstrate that methanethiolsulfonate (MTS) reagents form disulfide bonds with s4U more efficiently than the commonly used HPDP-biotin, leading to higher yields and less biased enrichment. This increase in efficiency allowed us to use s4U-labeling to study global microRNA (miRNA) turnover in proliferating cultured human cells without perturbing global miRNA levels or the miRNA processing machinery. This improved chemistry will enhance methods that depend on tracking different populations of RNA such as 4-thiouridine-tagging to study tissue-specific transcription and dynamic transcriptome analysis (DTA) to study RNA turnover.
Overall design s4U metabolic labeling of RNA in 293T cells, followed by biochemical enrichment of labeled RNA with two biotinylation reagents, RNAs >200nt and miRNAs in separate experiments
Contributor(s) Duffy EE, Rutenberg-Shoenberg M, Stark CD, Kitchen RR, Gerstein MB, Simon MD
Citation(s) 26340425
Submission date Sep 02, 2014
Last update date May 15, 2019
Contact name Erin Elizabeth Duffy
Phone (617)432-7795
Organization name Harvard Medical School
Department Neurobiology
Lab Michael E. Greenberg
Street address 200 Longwood Ave, Goldenson 405
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (24)
GSM1495268 Input 1
GSM1495269 Input 2
GSM1495270 HPDP-biotin
BioProject PRJNA260045
SRA SRP045983

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
GSE60988_RAW.tar 600.8 Mb (http)(custom) TAR (of BEDGRAPH)
GSE60988_miRNA_differential_expression_edgeR.xlsx 72.0 Kb (ftp)(http) XLSX
GSE60988_miRNA_quantifications_s4U.xlsx 237.9 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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